426 REFERENCES

Artwick, B. A. (1984). Applied Concepts in Microcomputer Graphics. Englewood Cliffs, NJ: Prentice Hall. Augustine, J. R., T. Huntsberger, and M. Moore (1985). Computer-aided reconstructive morphology of the

baboon abducens nucleus. Anat. Rec. 212:210-217. Axen, R., J. Porath, and S. Emback (1967). Chemical coupling of peptide and proteins to polysaccharides by

means of cyanogen halides. Nature 214:1302-1304. Badler, N. I., K. H. Maanoocherhri, and G. Walters (1987). Articulated figure positioning by multiple con­

traints. IEEE Comput. Graphics Appl. 7:28-38. Baker, H., A. F. Sved, L. W. Tucker, S. M. Alden, and D. J. Reis (1985). Strain differences in pituitary

prolactin content: Relationship to number of hypothalamic dopamine neurons. Brain Res. 358:16-26. Batschelet, E. (1981). Circular Statistics in Biology. London: Academic Press. Becker, L. E., D. L. Armstrong, and F. Chan (1986). Dendritic atrophy in children with Down's syndrome.

Ann. Neurol. 20:520-526. Bellinger, D. L., and W. J. Anderson (1987). Postnatal development of cell columns and their associated

dendritic bundles in the lumbosacral spinal cord of the rat. I. The ventrolateral cell column. Dev. Brain Res. 35:55-67.

Benno, R. H., L. W. Tucker, T. H. Joh, and D. J. Reis (1982a). Quantitative immunocytochemistry of tyrosine hydroxylase in rat brain. I. Development of a computer-assisted method using the peroxidase-antiperox­idase technique. Brain Res. 246:225-236.

Benno, R. H., L. W. Tucker, T. H. Joh, and D. J. Reis (1982b). Quantitative immunocytochemistry of tyrosine hydroxylase in rat brain. II. Variations in the amount of tyrosine hydroxylase among individual neurons of the locus coemleus in relationship to neuronal morphology and topography. Brain Res. 246:237-247.

Beran, R. J. (1968). Testing for uniformity on a compact homogeneous space. J. Appl. Prob. 5:177-195. Berry, M., and R. Flinn (1984). Vertex analysis of Purkinje cell dendritic trees in the cerebellum of the rat.

Proc. R. Soc. Lond. [Biol.J 221:321-348. Biegon, A., and M. Wolff (1986). Quantitative histochemistry of acetylcholinesterase in rat and human brain

postmortem. J. Neurosci. Methods 16:39-45. Bigbee, J. W., J. C. Kosek, and L. F. Eng (1977). Effects of primary antiserum dilution on staining of antigen­

rich tissues with the peroxidase antiperoxidase technique. J. Histochem. Cytochem. 25:443-447. Blackstad, T. W., K. K. Osen, and E. Mugnaini (1984). Pyramidal neurones of the dorsal cochlear nucleus: A

Golgi and computer reconstruction study in cat. Neuroscience 13:827-854. Blaisdel, G. (1986). Voltage-sensitive dyes reveal a modular organization in monkey striate cortex. Nature 321:

579-585. Boast, C. A., E. W. Snowhill, and C. A. Altar (1986). Quantitative Receptor Autoradiography. New York:

Alan R. Liss. Boivie, J. G., G. Grant, and H. Ulfendahl (1968). The X-Y recorder used for mapping under the microscope.

Acta Physiol. Scand. 74:AI-A2. Bok, S. T. (1959). Histonomy of the Cerebral Cortex. Amsterdam: Elsevier. Borges, S., and M. Berry (1978). The effects of dark rearing on the development of the visual cortex of the rat.

J. Compo Neurol. 180:277-300. Born, G. (1883). Die Plattenmodellirmethode. Arch. Mikrosk. Anat. 22:584-599. Boyle, P. J. R., and D. G. Whitlock (1974). The application of a computer controlled microscope to auto­

radiographs of nerve tissue. DECUS Proc. 1(2):95-99. Boyle, P. J. R., and D. G. Whitlock (1977). A computer-controlled microscope as a device for evaluating

autoradiographs. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 133-148.

Braverman, M. S., and I. M. Braverman (1986). Three-dimensional reconstruction of objects from serial sections using a microcomputer graphics system. J. Invest. Dermatol. 86:290-294.

Bregman, B. S., and W. L. R. Cruce (1980). Normal dendritic morphology offrog spinal motoneurons: A Golgi study. J. Compo Neurol. 193(4):1035-1045.

Briarty, L. G., J. Patrick, J. Fisher, and P. H. Jenkins (1982). Microscopy, morphology and microcomputers. Acta Stereol. 82:227-234.

Briski, K. P., B. L. Baker, and A. K. Christensen (1983). Effect of ovariectomy on the hypothalamic content of immunoreactive gonadotropin-releasing hormone in the female mouse as revealed by quantitative immu­nocytochemistry and radioimmunoassay. Am. J. Anat. 166:187-208.

Brooks, F. P., Jr. (1975). The Mythical Man-Month. Reading, MA: Addison-Wesley.

REFERENCES 427

Brooks, F. P., Jr. (1987). No silver bullet: Essence and accidents of software engineering. Computer 20(4):10-19.

Brown, C. (1977). Neuron orientations: A computer application. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 177-188.

Brown, P. B., ed. (1976). Computer Technology in Neuroscience. Washington, DC: Hemisphere. Brown, P. B., G. R. Busch, and J. Whittington (1979). Anatomical changes in cat dorsal hom cells after

transection of a single dorsal root. Exp. Neurol. 64:453-468. Buell, S. J., and P. D. Coleman (1979). Dendritic growth in the aged human brain and failure of growth in senile

dementia. Science 206:854-856. Buell, S. J., and P. D. Coleman (1981). Quantitative evidence for selective dendritic growth in normal human

aging but not in senile dementia. Brain Res. 214:23-41. Buskirk, D. R. (1978). Computer analysis of dendritic morphology. Brain Theor. Newsl. 3:184-186. Cahan, L. D., and B. T. Trombka (1975). Computer graphics three-dimensional reconstruction of thalamic

anatomy from serial sections. Comput. Prog. Biomed. 5:91-98. Cajal, S. R. (1906). Studien uber die Hirnrinde des Menschen. Leipzig: Verlag von Johann Ambrosius Barth. Cajal, S. R. (1909). Histologie du Systeme Nerveux de ['Homme et des Vertebres. Paris: Maloine. Cajal, S. R. (1984). The Neuron and the Glial Cell (Translated and edited by J. de la Torre and W. C. Gibson).

Springfield, IL: Charles C. Thomas. Calvet, M. C., and J. Calvet (1984). Computer assisted analysis of HRP-Iabelled and Golgi-stained Purkinje

neurons. Prog. Neurobiol. 23:251-272. Calvet, M. C., J. Calvet, and R. Camacho-Garcia (1985). The Purkinje cell dendritic tree: A computer-aided

study of its development in the cat and in culture. Brain Res. 331:235-250. Cameron, W. E., D. B. Averill, and A. J. Berger (1985). Quantitative analysis of the dendrites of cat phrenic

motoneurons stained intracellularly with horseradish peroxidase. J. Compo Neurol. 230:91-101. Capel, P. J. A. (1974). A quantitative immunofluorescence method based on the covalent coupling of protein to

sepharose beads. J. Immunol. Methods 5:165-178. Capowski, J. J. (1973). A general purpose 3D physical modeling program. Comput. Graphics 7(3):24-28. Capowski, J. J. (1976). Characteristics of neuroscience computer graphics displays and a proposed system to

generate those displays. Comput. Graphics 10(2):257-261. Capowski, J. J. (1977). Computer-aided reconstruction of neuron trees from several serial sections. Comput.

Biomed. Res. 10:617-629. Capowski, J. J. (1978a). The neuroscience display processor. Computer 11(11):48-58. Capowski, J. J. (1978b). The neuroscience display processor model 2. DECUS Proc. 5(2):763-766. Capowski, J. J. (1979). The modeling, display, and analysis of nerve cells. DECUS Proc. 6(2):739-742. Capowski, J. J. (1983a). An automatic neuron reconstruction system. J. Neurosci. Methods 8(4):353-

364. Capowski, J. J. (1983b). The neuroscience display processor model 3. DECUS Proc. 10(2):167-170. Capowski, J. J. (1985). The reconstruction, display, and analysis of neuronal structure using a computer. In: The

Microcomputer in Cell and Neurobiology Research CR. R. Mize, ed.). New York: Elsevier, pp. 85-109. Capowski, J. J. (1987). A new comprehensive neuron reconstruction system. system. Neurosci. 22(supp.):

S369. Capowski, J. J. (1988). Computer graphics display processor for generating dynamic refreshed vector images.

U.S. Patent 4,736,330. Capowski, J. J. (1988b). Anatomical measurement and analysis. In: Microcomputers in Physiology: A Practical

Approach (P. J. Fraser, ed.). Oxford: IRL Press, pp. 95-127. Capowski, J. J., and W. L. R. Cruce (1979). How to configure a computer-aided neuron reconstruction and

graphics display system. Comput. Biomed. Res. 12(6):569-587. Capowski, J. J., and W. L. R. Cruce (1981). The personnel needs of a neuroscientific computer center. SIGBIO

Newsletter special issue March: 110-128. Capowski, J. J., and E. M. Johnson (1985). A simple hidden line removal algorithm for serial section recon­

struction. J. Neurosci. Methods 13:145-152. Capowski, J. J., and M. Rethelyi (1978). Computer analysis of the distribution of synaptic elements of Golgi­

stained axon trees. Brain Theory Newsl. 3:179-183. Capowski, J. J., and M. Rethelyi (1982). Neuron reconstruction using a Quantimet image analyzing computer.

Acta Morphol. Sci. Hung. 30:243-251.

428 REFERENCES

Capowski, J. J., and S. A. Schneider (1985). A simple motor controller for computer-assisted microscopy. 1. Neurosci. Methods 13:97-102.

Capowski, J. J., and M. J. Sedivec (1981). Accurate computer reconstruction and graphics display of complex neurons utilizing state-of-the-art interactive techniques. Comput. Biomed. Res. 14:518-532.

Capowski, 1. J., M. 1. Sedivec, and L. M. Mendell (1986). An illustration of spinocervical tract cells and their computer reconstruction. 1. Neurosci. 6(3):front cover.

Carr, D. B., W. L. Nicholson, R. 1. Littlefield, and D. L. Hall (1986). Interactive color display methods for multivariate data. In: Statistical Image Processing and Graphics (E. J. Wegman and D. J. DePriest, eds.). New York: Marcel Dekker.

Casale, E. J. (1988). Anatomy and Physiology of Corticospinal Tract Neurons in the Rat and Cat. Doctoral Dissertation, University of North Carolina.

Cassell, M. D., N. 1. Mankovich, T. S. Gray, and T. H. Williams (1982). Computer-assisted image analysis of the distributions of peptidergic terminals in the central nucleus of the amygdala: A preliminary study. Peptides 3:283-290.

Castleman, K. R. (1979). Digital Image Procesing. Englewood Cliffs, NJ: Prentice Hall. Chatfield, c., and A. 1. Collins (1980). Introduction to Multivariate Analysis. London: Chapman and Hall. Chawla, S. D., L. Glass, and J. W. Procter (1981). Three-dimensional reconstruction of disseminated cancer

modules. Cancer Biochem. Biophys. 5:153-161. Chawla, S. D., L. Glass, S. Friewald, and J. W. Procter (1982). An interactive computer graphic system for 3-D

steroscopic reconstruction from serial sections: Analysis of metastatic growth. Comput. Bioi. Med. 12(3): 223-232.

Claiborne, B. J., D. G. Amaral, and W. M. Cowan (1986). A light and electron microscopic analysis of the mossy fibers of the rat dentate gyrus. 1. Compo Neuol. 246(4):435-458.

Cochran, W. G. (1977). Sampling Techniques, 3rd ed. New York: John Wiley & Sons. Coleman, P. D., and D. G. Flood (1987). Neuron numbers and dendritic extent in normal aging and Alzheimer's

disease. Neurobiol. Aging 8:521-545. Coleman, P. D., C. F. Garvey, J. H. Young, and W. Simon (1977). Semiautomatic tracing of neuronal

processes. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 91-109.

Coleman, P. D., D. G. Flood, M. C. Whitehead, and R. C. Emerson (1981). Spatial sampling by dendritic trees in visual cortex. Brain Res. 214:1-21.

Colonnier, M. (1964). The tangential organization of the visual cortex. 1. Anat. 98:327-344. Comans, P. E., I. S. McLennan, R. F. Mark, and I. A. Hendry (1988). Mammalian motoneuron development:

Effect of peripheral deprivation on motoneuron numbers in a marsupial. 1. Compo Neurol. 270(1):111-120.

Conover, W. J. (1980). Practical Nonparametric Statistics, 2nd ed. New York: John Wiley & Sons. Conover, W. 1., and R. L. Iman (1981). Rank transformations as a bridge between parametric and non­

parametric statistics. Am. Stat. 35:124-133. Coombs, G. H., L. Tetley, V. A. Moss, and K. Vickerman (1986). Three dimensional structure of the

leishmania amastigote as revealed by computer-aided reconstruction from serial sections. Parasitology 92: 13-23.

Comelisse, 1. T. W. A., and T. 1. T. P. van den Berg (1984). Profile boundary length can be overestimated by as much as 41% when using a digitizer tablet. 1. Microsc. 136(3):341-344.

Cowan, W. M., and D. F. Wann (1973). A computer system for the measurement of cell and nuclear sizes. 1. Microsc. (04'.) 99:331-448.

Cruce, W. L. R., and S. L. Steusse (1987). Three-dimensional neuron reconstruction: A retrospective view of ten years' use in the anatomical laboratory. Neurosci. 22(suppl):S393.

Cruz-Orive, L.-M., and E. B. Hunziker (1986). Stereology for anisotropic cells: Application to growth car­tilage. 1. Microsc. (Oxf.) 143:47-80.

CUllheim, S., 1. W. Fleshman, L. L. Glenn, and R. E. Burke (1987a). Membrane area and dendritic structure in type-identified triceps surea alpha motoneurons. 1. Compo Neurol. 255:68-81.

Cullheim, S., J. W. Fleshman, L. L. Glenn, and R. E. Burke (1987b). Three-dimensional architecture of dendritic trees in type-identified a-motoneurons. 1. Comp. Neurol. 255:82-96.

Curcio, C. A., and K. R. Sloan (1981). A computer system for combined neuronal mapping and morphometry. 1. New·osci. Methods 4:267-276.

REFERENCES 429

Curcio, C. A., and K. R. Sloan (1986). Computer-assisted morphometry using video-mixed microscopic images and computer graphics. Anal. Rec. 214:329-337.

Dann, J. F., and E. H. Buhl (1987). Retinal ganglion cells projecting to the accessory optic system in the rat. J. Compo Neurol. 262:141-158.

Davis, B. J. (1985). The electronic pantograph: Amplifier couples microscope stage toX-Yplotter. Brain Res. Bull. 15:533-536.

DePasquale, J. D., and C. S. Izzard (1987). Evidence for an actin-containing cytoplasmic precursor of the focal contact and the timing of incorporation of vinculin at the focal contact. J. Cell BioI. 105:2803-2809.

De Ruiter, J. P., and H. B. M. Uylings (1987). Morphometric and dendritic analysis of fascia dentata granule cells in human aging and senile dementia. Brain Res. 402:217-229.

DeVoogd, T. J., F. L. F. Chang, M. K. Floeter, M. J. Jencius, and W. T. Greehough (1981). Distortions induced in neuronal quantification by camera lucida analysis: Comparisons using a semiautomated data acquisition system. J. Neurosci. Methods 3:284-294.

Dierker, M. L. (1976a). An algorithm for the alignment of serial sections. In: Computer Technology in Neuroscience (P. B. Brown, ed.). Washington, DC: Hemisphere, pp. 131-133.

Dierker, M. L. (1976b). An algorithm for the display and manipulation of lines in three dmensions. In: Computer Technology in Neuroscience (P. B. Brown, ed.). Washington, DC: Hemisphere, pp. 139-151.

Dinopoulos, A., J. G. Pamavelas, H. B. M. Uylings, and C. G. Van Eden (1988). Morphology of neurons in the basal forebrain nuclei of the rat: A Golgi study. J. Compo Neurol. 272:461-474.

Dunn, R. F., O'Leary, D. P., and Kurnley, W. E. (1975). Quantitative analysis of micrographs by computer graphics. J. Microsc. (Oxf) 105:205-213.

Dunn, R. F., D. P. O'Leary, and W. E. Kumley (1977). Online computerized analysis of peripheral nerves. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 111-132.

DuVamey, D., and R. C. DuVamey (1985). A computer-based video microscope. In: The Microcomputer in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 233-246.

Dykes, E., and F. Afshar (1982). Computer generated three dimensional reconstructions from serial sections. Acta Sterol. 82:289-296.

Dykes, E., and J. G. Clement (1980). The construction and application of an X-Y coordinate plotting micro­scope. J. Dent. Res. 59:1800.

Eayrs, J. T. (1955). The cerebral cortex of normal and hypothyroid rats. Acta Anat. 25:160-183. Eidelberg, E., and F. Davis (1977). An improved electronic pantograph. J. Histochem. Cytochem. 25:1016-

1018. Ellias, S. A., and J. K. Stevens (1980). The dendritic varicosity: A mechanism for electrically isolating the

dendrites of cat retinal amacrine cells? Brain Res. 196:365-372. Eilisman, M., R. Ranganathan, T. Deerinck, S. Young, R. Terry, and S. Mirra (1987). Neuronal fibrillar

cytoskeleton and endomembrane system organization in Alzheimer's disease. In: Alterations in the Neu­ronal Cytoskeleton in Alzheimer's Disease (G. Perry, ed.). New York: Plenum Press, pp. 61-73.

Eysel, U. T., L. Peichl, and H. Wassle (1985). Dendritic plasticity in the early postnatal feline retina: Quan­titative characteristics and sensitive period. J. Compo Neurol. B242:134-145.

Fahle, M. (1988). The double microscope: Its use in three-dimensional reconstruction from serial sections. J. Neurosci. Methods 23:95-99.

Falck, B., N. A. Hillarp, G. Thieme, and A. Thorpe (1962). Fluorescence of catecholamines and related compounds condensed with formaldehyde. J. Histochem. Cytochem. 10:348-354.

Falen, S. W., and D. S. Packard, Jr. (1982). Computer-assisted stereoscopic reconstruction of biological tissues. Proc. Natl. Com put. Graphics Assn. 2:995-1003.

Feingold, E., S. B. Seshadri, and O. J. Tretiak (1986). Hardware and software design consideration in engineering and image processing workstation: Autoradiographic analysis with DUMAS and the BRAIN

autoradiograph analysis software package. In: Functional Mapping in Biology and Medicine: Computer Assisted Autoradiography (D. L. McEachron, ed.). Basel: Karger, pp. 175-203.

Fisher, J. B., and H. Honda (1977). Computer simulation of branching pattern and geometry in terminalia (combretaceae), a tropical tree. Bot. Gaz. 138(4):377-384.

Flaming, D. G. (1982). A short review of current laboratory microcomputer systems and practice. J. Neurosci. Methods 51:1-6.

Flaming, D. G. (1985). CP/M and programming languages. In: Microcomputers in the Neurosciences (G. A. Kerkut, ed.). Oxford: Clarendon Press, pp. 142-151.

430 REFERENCES

Flood, D. G., S. J. Buell, G. J. Horwitz, and P. D. Coleman (1987). Dendritic extent in human dentate gyrus granule cells in normal aging and senile dementia. Brain Res. 402:205-216.

Foley, J. D., and A. van Dam (1982). Fundamentals of Interactive Computer Graphics. Reading, MA: Addison-Wesley.

Foley, J. D., and V. L. Wallace (1974). The art of natural graphic man-machine conversation. Proc.IEEE 62: 462-471.

Foley, J. D., V. L. Wallace, and P. Chan (1984). The human factors of computer graphics interaction techniques. IEEE Comput. Graphics Appl. 4(11):13.

Foote, S. L., S. E. Loughlin, P. S. Cohen, F. E. Bloom, and R. B. Livingston (1980). Accurate three­dimensional reconstruction of neuronal distributions in brain: Reconstruction of the rat nucleus locus coeruleus. J. Neurosci. Methods 3:159-173.

Forbes, D. J., and R. W. Petry (1979). Computer-assisted mapping with the light microscope. J. Neurosci. Methods 1:77-94.

Ford-Holevinski, T. S., T. A. Dahlberg, and B. W. Agranoff (1986). A Microcomputer-based image analyzer for quantitating neurite outgrowth. Brain Res. 368:339-346.

Fram, E. K. (1985). 3-D reconstruction: Seeing beyond the surface. PC Magazine Aug 20:170-174. Franltois, C., J. Yeluik, and G. Percheron (1987). Golgi study of the primate substantia nigra. II. Spatial

organization of dendritic arborizations in relation to the cytoarchitectonic boundaries and to the striatonigrai bundle. J. Compo Neurol. 265:473-493.

Frasch, A. C. C., M. E. Itoiz, and R. L. Cabrini (1978). Microspectrophotometric quantitation of the di­aminobenzidine reaction for histochemical demonstration of cytochrome oxidase activity. J. Histochem. Cytochem. 26:157-162.

Freeman, J., and R. S. Meltzer (1983). CARTOS revives biological approach from turn of century. Comput. Graphics News May/June:17-18.

Freiherr, G. (1987). Image combining microscope resource. Research Resources Reporter. U.S. Heath and Human Services 12(12):13-14.

Freire, M. (1986). An inexpensive and interactive microcomputer system for codifying Golgi-impregnated neuronal morphology. J. Neurosci. Methods 16:103-117.

Frenkel, K. A. (1988). The art and science of visualizing data. Commun. ACM 31(2):110-122. Gage, S. H. (1941). The Microscope. Ithaca, NY: Comstock. Gallistel, C. R., and O. Tretiak (1985). Microcomputer systems for analyzing 2-deoxyglucose autoradiographs.

In: The Microcomputer in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 379-408.

Gambino, D. R., L. T. Malmgren, and R. R. Gacek (1985). Three-dimensional computer reconstruction of the neuromuscular junction distribution in the human posterior cricoarytenoid muscle. Laryngoscope 95(5): 556-560.

Garvey, C. F., J. Young, W. Simon, and P. D. Coleman (1972). Semiautomatic dendrite tracking and focusing by computer. Anat. Rec. 172:314.

Garvey, C. F., J. Young, W. Simon, and P. D. Coleman (1973). Automated three-dimensional dendrite tracking system. Electroencephalogr. Clin. Neurophysiol. 35:199-204.

Gaunt, P. N., and W. A. Gaunt (1978). Three-Dimensional Reconstruction in Biology. Tunbridge Wells: Pitman.

Gdowski, G. T., W. D. Eldred, and H. F. Voight (1987). A simple device for the computer quantification of depth measurements in thick light microscope sections. J. Neurosci. Methods 20:249-260.

Geffard, M., A. M. Henrich-Rock, H. Dulluc, and P. Seguela (1985). Antisera against small neurotransmitter­like molecules. Neurochem. Int. 7:403-413.

Geisow, M. J., and A. N. Barrett, eds. (1983). Computing in Biological Sciences. Amsterdam: Elsevier Biomedical Press.

Gentile, A. M., and E. Harth (1978). The alignment of serial sections by spatial filtering. Com put. Biomed. Res. 11:537-551.

German, D. C., D. S. Schlusselberg, and D. J. Woodward (1983). Three-dimensional computer reconstruction of midbrain dopaminergic neuronal popUlations: From mouse to man. Neural Transm. 57:243-254.

GerOcs, K., M. Rethelyi, and B. Halasz (1986). Quantitative analysis of dendritic protrusions in the medial preoptic area during postnatal development. Dev. Brain Res. 26:49-57.

REFERENCES 431

Giloi, W. K. (1978). Interactive Computer Graphics; Data Structures, Algorithms, Languages. Englewood Cliffs, NJ: Prentice-Hall.

Glaser, E. M. (1981). A binary identification system for use in tracing and analyzing dichotomously branching dendrite and axon systems. Comput. BioI. Med. 11:17-19.

Glaser, E. M. (1982). Snell's law: The bane of computer microscopists. J. Neurosci. Methods 5:201-202. Glaser, E. M., and N. T. McMullen (1984). The fan-in projection method for analyzing dendrite and axon

systems. J. Neurosci. Methods 12:37-42. Glaser, E. M., and H. van der Loos (1965). A semiautomatic computer microscope for the analysis of neuronal

morphology. IEEE Trans. Biomed. Eng. 12:22-31. Glaser, p. M., and H. van der Loos (1980). Computer microscope apparatus and method for superimposing an

elee:tronically-produced image from the computer memory upon the image in the microscope's field of view. U.S. Patent 4,202,037.

Glaser, E. M., and H. van der Loos (1981). Analysis of thick brain sections by obverse-reverse computer microscope: Application of a new, high clarity Golgi-Nissl stain. J. Neurosci. Methods 4:117-125.

Glaserj E. M., H. van der Loos, and M. Gissler (1978). Preferred tangential orientation and spatial order in dendritic fields of cat auditory cortex: A computer-microscope study of Golgi-stained material. Soc. Neurosci. Abstr. 4:210.

Glaser, E. M., M. Gissler, and H. van der Loos (1979a). An interactive camera lucida computer-microscope. Soc. Neurosci. Abstr. 5:1697.

Glaser, E. M., H. Van der Loos, and M. Gissler (1979b). Tangential organization and spatial order in dendrites of cat auditory cortex: A computer microscope study of Golgi-impregnated material. Exp. Brain Res. 36: 411-431.

Glaser, E. M., M. Tagamets, N. T. McMullen, and H. van der Loos (1983). The image-combining computer mifroscope-an interactive instrument for morphometry of the nervous system. J. Neurosci. Methods 8: 17-32.

Glasser, S., J. Miller, N. G. Xuong, and A. Selverston (1977). Computer reconstruction of invertebrate nerve cells. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 21-58.

Glenn, L. L., and R. E. Burke (1981). A simple and inexpensive method for 3-dimensional visualization of neurons reconstructed from serial sections. J. Neurosci. Methods 4:127-134.

Gonzales, R. C., and P. W. Wintz (1977). Digital Image Processing. Reading, MA: Addison-Wesley. Goochee, C., W. Rasband, and L. Sokoloff (1979). Computerized densitometry and color coding of 14C_

deQxyglucose autoradiographs. Ann. Neurol. 7:359-370. Graham, R. C., and M. J. Karnovsky (1966). The early stages of absorption of injected horseradish peroxidase.

in the proximal tubules of mouse kidney: Ultrastructural cytochemistry by a new technique. J. Histochem. Cytochem. 14:291-302.

Gras, H. (1984). A "hidden line" algorithm for 3D-reconstruction from serial sections-An extension of the NEUREC program package for a microcomputer. Comput. Prog. Biomed. 18:217-226.

Gras, H., and F. Killman (1983). NEUREc-a program package for 3-D reconstruction from serial sections using a microcomputer. Comput. Prog. Biomed. 17:145-156.

Graveland, G. A., R. S. Williams, and M. DiFiglia (1985). A Golgi study ofthe human neostriatum: Neurons and afferent fibres. J. Compo Neurol. 234:317-333.

Greenberg, M., J. Stevens, and S. Ellias (1985). Highly irregular shapes of normal type C axons: Serial EM study. Soc. Neurosci. Abstr. 11:184.4.

Greenough, W. T., and F. R. Volkmar (1973). Pattern of dendritic branching in occipital cortex ofrats reared in complex environments. Exp. Neurol. 40:491-504.

Greenough, W. T., C. S. Carter, C. Steerman, and T. J. De Voogd (1977). Sex differences in dendritic patterns in hamster preoptic area. Brain Res. 126:63-72.

Gross, D. S., and 1. M. Rothfeld (1985). Quantitative immunocytochemistry of hypothalamic and pituitary hormones: Validation of an automated, computerized image analysis system. J. Histochem. Cytochem. 33: 11-20.

Gundersen, H. J. G., and R. Osterby (1981). Optimizing sampling efficiency of stereological studies in biology: Or "Do more less well!" J. Microsc. (Oxj.) 121:65-73.

Gupta, M., T. M. Mayhew, K. S. Bedi, A. K. Sharma, and F. H. White (1982). Inter-animal variation and its

432 REFERENCES

influence on the overall precision of morphometric estimates based on nested sampling designs. J. Microsc. (Oxf.) 131:147-154.

Haberly, L. B. (1983). Structure of the piriform cortex of the opossum. I. Description of neuron types with Golgi methods. J. Compo Neurol. 213:163-187.

Haberly, L. B., and J. M. Bower (1982). Graphical methods for three-dimensional rotation of complex axonal arborizations. J. Neurosci. Methods 6:75-84.

Hansen. W. J. (1971). User engineering principles for interactive systems. In: Proceedings of the Fall Joint Computer Conference. Montvale, NJ: AFIPS Press.

Harding, E. F. (1971). The probabilities of rooted tree-shapes generated by random bifurcation. J. Appl. Prob. 3:44-77.

Harms, H., and H. M. Aus (1984). Comparison of digital focus criteria for a TV microscope system. Cytometry 5:236-243.

Harpring, J. E., J. C. Pearson, J. R. Norris, and B. L. Mann (1985). Subclassification of neurons in the ventrobasal complex of the dog: Quantitative Golgi study using principal component analysis. J. Compo Neurol. 242:230-246.

Harris, K. M., and J. K. Stevens (1988). Study of dendritic spines by serial electron microscopy and three­dimensional reconstructions. In: Intrinsic Determinants of Neuronal Form and Function (R. J. Lasek and M. M. Black, eds.). New York: Alan R. Liss, pp. 179-199.

Hartman, M. L., A. J. Beitz, J. E. Madl, and R. R. Mize (1988). Glutamate-like antibody staining in the cat superior colliculus is reduced by visual decortication. Invest. Ophthalmol. Vis. Sci. [Suppl]. 29:32.

Hengstenberg, R., H. Bulthoff, and B. Hengstenberg (1983). Three-dimensional reconstruction and ster­eoscopic display of neurons in the fly visual system. In: Functional Neuroanatomy (N. J. Strausfeld, ed.). Berlin: Springer-Verlag, pp. 183-205.

Henson, O. W., and M. M. Henson (1986). Morphometric analysis of cochlear structures in the mustached bat, Pteronotus parnellii parnellii. In: 3rd International Symposium on Animal Sonar Systems. Helsingor, Denmark. New York: Plenum Press, pp. 301-305.

Hibbard, L. S., and R. A. Hawkins (1984). Three-dimensional reconstruction of metabolic data from quan­titative autoradiography of rat brain. Am. J. Physiol. 247:E412-E419.

Hibbard, L. S., and R. A. Hawkins (1988). Objective image alignment for three-dimensional reconstruction of digital autoradiograms. J. Neurosci. Meth. 26:55-74.

Hibbard, L. S., J. S. McGlone, D. W. Davis, and R. A. Hawkins (1987). Three-dimensional representation and analysis of brain energy metabolism. Science 236:1641-1646.

Hillman, D. E. (1976). A tridimensional reconstruction computer system for neuroanatomy. Comput. Med. 5(6): 1-2.

Hillman, D. E. (1979). Neuronal shape parameters and substructures as a basis of neuronal form. In: The Neuroscience Fourth Study Program (F. O. Schmitt and F. G. Worden, eds.). Cambridge, MA: MIT Press, pp. 477-498.

Hillman, D. E., R. Llinas, and M. Chujo (1977). Automatic and semiautomatic analysis of nervous system structure. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp.73-90.

His, W. (1880). Anatomie Menschlicher Embryonen. Leipzig: Vogel. Hitchcock, P. F., and S. S. Easter, Jr. (1986). Retinal ganglion cells in goldfish: Qualitative classification into

four morphological types, and a quantitative study of the development of one of them. J. Neurosci. 6(4): 1037-1050.

Hofman, M. A., A. C. Laan, and H. B. M. Uylings (1986). Bivariate linear models in neurobiology: Problems of concept and methodology. J. Neurosci. Methods 18:103-114.

Hogan, R. N., and P. D. Coleman (1981). Experimental hyperphenylalaninemia: Dendritic in motor cortex of rat. Exp. Neurol. 74:218-233.

Holdefer, R. N., T. T. Norton, and R. R. Mize (1988). Laminar organization and ultrastructure of GAB A­immunoreactive neurons and processes in the dorsal lateral geniculate nucleus of the tree shrew (Tupaia belangeri). Vis. Neurosci. 1:189-204.

Hollingworth, T., and M. Berry (1975). Network analysis of dendritic fields of pyramidal cells in neocortex and Purkinje cells in the cerebellum of the rat. Phil. TrailS. R. Soc. Lond. [Bioi.] 270:227-264.

Honda, H., and J. B. Fisher (1978). Tree branch angle: Maximizing effective leaf area. Science 199:888-890.

REFERENCES 433

Horsfield, K. (1980). Are diameter, length and branching ratios meaningful in the lung? J. Theor. Bioi. 87:773-784.

Horsfield, K., and M. J. Woldenberg (1986). Comparison of vertex analysis and branching ratio in the study of trees. Respir. Physiol. 65:245-256.

Horwitz, B. (1981). Neuronal plasticity: How changes in dendritic architecture can affect the spread of postsynaptic potentials. Brain Res. 224:412-418.

Houser, C. R., A. B. Harris, and J. E. Vaughn (1986). Time course of the reduction of GABA tenninals in a model of focal epilepsy: A glutamic acid decarboxylase immunocytochemical study. Brain Res. 383: 129-145.

Hsu, S. M., L. Raine, and H. Fanger (1981). A comparative study of the peroxidase-antiperoxidase method and an aviden-biotin complex method for studying polypeptide honnones with radioimmunoassay antibodies. Am. J. Clin. Pathol. 75:734-738.

Huijsmans, D. P. (1983). Closed 2D contour algorithms for 3D reconstruction. In: Eurographics • 83 Conference Proceedings (P. J. W. ten Hagen, ed.). Amsterdam: Elsevier, pp. 157-168. .

Huijsmans, D. P., W. H. Lamers, J. A. Los, J. Smith, and J. Strackee (1984). Computer-aided three­dimensional reconstruction from serial sections: A software package for reconstruction and selective image generation for complex topologies. In: Eurographics ' 84 Conference Proceedings. (K. Bo and H. Tucker, eds.). Amsterdam: Elsevier, pp. 3-13.

Huijsmans, D. P., W. H. Lamers, J. A. Los, and J. Strackee (1986). Toward computerized morphometric facilities: A review of 58 software packages for computer-aided three-dimensional reconstruction, quan­tification and picture generation from parallel serial sections. Anat. Rec. 216:449-470.

Hull, C. D., 1. P. McAllister, M. S. Levine, and A. M. Adinolfi (1981). Quantitative developmental studies of feline neostriatal spiny neurons. Dev. Brain Res. 1:309-332.

Inoue, S. (1986). Video Microscopy. New York: Plenum Press. Ipifta, S. L. (1987). A multivariate phenetic approach to neuronal nuclei; resemblances across species, with

examples from three regions of cerebral cortex of a manunal, a bird and a reptile. J. Theor. Bioi. 126:105-124.

Ipifta, S. L., and A. Ruiz-Marcos (1986). Dendritic structure alterations induced by hypothyroidism in pyra­midal neurons of the rat visual cortex. Dev. Brain Res. 29:61-67.

Ipifta, S. L., A. Ruiz-Marcos, F. Escobar del Rey, and G. Morreale de Escobar (1987). Pyramidal cortex cell morphology studied by multivariate analysis: Effects of neonatal thyroidectomy, ageing and thyroxine substitution therapy. Dev. Brain Res. 37:219-229.

Ireland, W., J. Heidel, and E. Uemura (1985). A mathematical model for the growth of dendritic trees. Neurosci. Lett. 54:243-249.

Jacobs, J. R., and J. K. Stevens (1986). Changes in the organization of the neuritic cytoskeleton during nerve growth factor-activated differentiation of the PC12 cells: A serial electron microscopic study of the devel­opment and control of neurite shape. J. Cell Bioi. 103:895-906.

Jarvis, R. S., and A. Werritty (1975). Some comments on testing random topology stream network models. Water Resources Res. 11:309-318.

Jarvis, R. S., and M. J. Woldenberg (1984). River Networks. Benchmark Papers in Geology/80. Stroudsberg, PA: Hutchinson Ross.

Jimenez, J., A. Santisteban, J. M. Carazo, and J. L. Carrascosa (1986). Computer graphic display method for visualizing three-dimensional biological structures. Science 232:1113-1115.

Johnson, E. M., and J. J. Capowski (1983). A system for the three-dimensional reconstruction of biological structures. Comput. Biomed. Res. 16:79-87.

Johnson, E. M., and J. J. Capowski (1985). Principles of reconstruction and three-dimensional display of serial sections using a computer. In: The Microcomputer in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 249-263.

Jones, E. G. (1975). Varieties and distribution of non-pyramidal cells in the somatic sensory cortex of the squirrel monkey. J. Compo Neurol. 160:205-268.

Jones, S. C., and D. Lu (1988). The evaluation of quantitative autoradiogram processing systems for cere­brovascular research. J. Neurosci. Methods 24(1):1l-25.

Jones, W. H., and D. B. Thomas (1962). Changes in the dendritic organization of neurons in the cerebral cortex following deafferentiation. J. Anat. 96:375-381.

434 REFERENCES

Juraska, J. M. (1984). Sex differences in developmental plasticity in the visual cortex and the hippocampal dentate gyrus. In: Sex Differences in the Brain, Progress in Brain Research, Vol. 61 (G. J. de Vries, J. P. C. de Bruin, H. B. M. Uylings, and M. A. Corner, eds.). Amsterdam: Elsevier, pp. 205-214.

Juraska, J. M., W. T. Greenough, C. Elliot, K. J. Mack, and R. Berkowitz (1980). Plasticity in adult rat visual cortex: An examination of several cell populations after differential rearing. Behav. Neurol. Bioi. 29: 157-167.

Kapps, C., and L. Mays (1978). An inexpensive system for digitizing pictoral information. DECUS Proc. 5(2): 735-749.

Kastschenko, N. (1886). Methode zur genauen rekonstruktion kleinerer makroskopischer gegenstandb. Arch. Anat. Physiol. Abt. 1:388-394.

Kater, S. B., C. S. Cohan, G. A. Jacobs, and J. P. Miller (1986). Image intensification of stained, functioning, and growing neurons. In: Optical Methods in Cell Physiology (P. de Weer and B. M. Salzberg, eds.). New York: John Wiley & Sons, pp. 31-50. .

Katz, L. C. (1987). Local circuitry of identified projection neurons in cat visual cortex brain slices. 1. Neurosci. 7:1223-1249.

Katz, L., and C. Levinthal (1972). Interactive computer graphics and representation of complex biological structures. Ann. Rev. Biophys. Bioeng. 1:465-504.

Keppel, G. (1982). Design and Analysis. A Researcher's Handbook, 2nd ed. Englewood Cliffs, NJ: Prentice­Hall.

Kernell, D. (1966). Input resistance, electrical excitability and size of ventral horn cells in cat spinal cord. Science 152:1637-1640.

Kimura, 0., E. Dykes, and R. W. Fearnhead (1977). The relationship between the surface area of the enamel crowns of human teeth and that of the dentine-enamel junction. Arch. Oral Bioi. 22:677-683 ..

Kinnamon, 1. c., T. A. Sherman, and S. D. Roper (1988). Ultrastructure of mouse vallate taste buds: III. Patterns of synaptic connectivity. 1. Compo Neurol. 270:1-10.

Kropf, N., I. Sobel, and C. Levinthal (1985). Serial section reconstruction using CARTOS. In: The Microcom­puter in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 265-29~:

Kujoory, M. A., B. H. Mayall, an M. L. Mendelsohn (1973). Focus-assist device for a flying-spot microscope. IEEE Trans. Biomed. Eng. 20:126-132.

Kusinitz, M. (1987). 3-D nerve images made easy. New Med. Sci. 1(4):5-7. Lear, J. L., K. Mido, J. Plotnick, and R. Muth (1986). High-performance digital image analyzer for qU\lIltitative

autoradiography. 1. Cereb. Blood Flow Metab. 6:625-629. Leontovich, T. A. (1973). Methodik zur quantitativen Beschreibung subcorticaler Neurone. 1. Hirriforsch. 14:

59-87. Leuba, G., and L. J. Garey (1984a). Orientation of dendrites in the lateral geninculate nucleus of the monkey.

Exp. Brain Res. 56:369-376. Leuba, G., and L. J. Garey (1984b). Development of dendritic patterns in the lateral geniculate nucleus of the

monkey: A quantitative Golgi study. Dev. Brain Res. 16:285-299. Leventhal, A. G., and J. D. Schall (1983). Structural basis of orientation sensitivity of cat retinal ganglion cells.

1. Compo Neurol. 220:465-475. Levinthal, C., and R. Ware (1972). Three dimensional reconstruction from serial sections. Nature 236:207-

210. Levinthal, C., E. R. Macagno, and C. Tountas (1974). Computer-aided reconstruction from serial sections.

Fed. Proc. 33(12):2336-2340. Levinthal, F., E. R. Macagno, and C. Levinthal (1976). Anatomy and development of identified cells in

isogenic organisms. Cold Spring Harbor Symp. Quant. Bioi. XL:321-331. Lieth, E. (1987). Neuronal-Glial Interactions in CNS Development. Doctoral Dissertation, University of North

Carolina at Chapel Hil. Light, A. R., and A. M. Kavookjian (1988). Morphology and ultrastructure of physiologically identified

substantia gelatinosa (lamina II) neurons with axons that terminate in deeper dorsal horn laminae (III - IV). 1. Compo Neurol. 267:172-189.

Light, A. R., and E. R. Perl (1979). Spinal termination of functionally identified primary afferent neurons with slowly conducting myelinated fibers. J. Compo Neurol. 186(2):133-150.

Lindsay, R. D. (1977a). Computer analysis of neuronal structures. In: Computers in Biology and Medicine (G. P. Moore, ed.). New York: Plenum Press, pp. 71-79.

REFERENCES 435

Lindsay, R. D. (1977b). The video computer microscope and A.R.G.O.S. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 1-19.

Lindsay, R. D. (1977c). Tree analysis of neuronal processes. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 149-164.

Lindsay, R. D. (1977d). Neuronal field analysis using Fourier series. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 165-175.

Lindsay I R. D., and A. B. Scheibel (1976). Quantitative analysis of dendritic branching pattern of granular cells from human dentate gyrus. Exp. Neurol. 52:295-310.

Litzinger, B. E. (1988). VGA-campatible issues perplex board buyers. Comput. Technol. Rev. 8(3):1-6. Llinas, R., and D. E. Hillman (1975). A multipurpose tridimensional reconstruction computer system for

neuroanatomy. In: Golgi Centennial Symposium Proceedings (M. Santini, ed.). New York: Raven Press, pp.m-79.

Lopresti, V., E. R. Macagno, and C. Levinthal (1973). Structure and development of neuronal connections in isogenic organisms: Cellular interactions in the development of the optic lamina of Daphnia. Proc. Natl. Acad. Sci. U.S.A. 70(2):433-437.

Lund, J. S. (1973). Organisation of neurons in the visual cortex, area 17, of the monkey, Macaca mulatta. J. Compo Neurol. 147:455-496.

Macagno, E. R. (1978). Mapping synaptic sites between identified neuronsin leech CNS by means of 3-D computer reconstructions from serial sections. Brain Theory Newsl. 3(3/4):186-189.

Macagno, E. R., V. Lopresti, and C. Levinthal (1973). Structure and development of neuronal connections in isogenic organisms: Variations and similarities in the optic system of Daphnia magna. Proc. Natl. Acad. Sci. U.S.A. 70:57-61.

Macagno; E. R., C. Levinthal, C. Tountas, R. Bornholdt, and R. Abba (1976). Recording and analysis of 3-D information from serial section micrographs: The CARTOS system. In: Computer Technology in Neuro­science (P. B. Brown, ed.). Washington, DC: Hemisphere, pp. 97-112.

MacDon~ld, N. (1983). Trees and Networks in Biological Models. Chichester: John Wiley & Sons. Madri, J. A., and K. W. Barwick (1983). Use of avidin-biotin complex in an ELISA system: A quantitative

comparison with two other irnrnunoperoxidase detection systems using keratin antisera. Lab. Invest. 48: 98-107.

Mannen"H. (1966). Contribution to the quantitative study of the nervous tissue. A new method for measurement of the volume and surface area of neurons. J. Camp. Neurol. 126:75-89.

Mannen, H. (1975). Reconstruction of axonal trajectory of individual neurons in the spinal cord using Golgi­stained serial sections. J. Camp. Neural. 159:357-374.

Mannen, H., and Y. Sugiura (1975). Reconstruction of neurons of dorsal hom proper using Golgi-stained serial sections. J. Camp. Neural. 168:303-312.

March, S. c., I. Parikh, and P. Cuatrecasas (1974). A simplified method for cyanogen bromide activation of agarose for affinity chromatography. Anal. Biochem. 60:149-152.

Mardia, K. V. (1975). Statistics of directional data. J. R. Stat. Soc. B37:349-393. Marino, T. A., P. Nong Cook, L. T. Cook, and S. 1. Dwyer III (1980). The use of computer imaging techniques

to visualize cardiac muscle cells in three dimensions. Anat. Rec. 198:537-546. Marx, J. L. (1976). Computers: Helping to study nerve cell structure, Science 193:565-608. McEachron, D. (1986). Function Mapping in Biology and Medicine: Computer Assisted Autoradiography.

Basel: Karger. McEachron, D. L., C. R. Gallistel, 1. L. Eilbert, and 0.1. Tretiak (1988) The analytic and functional accuracy

of a video densitometry system. J. Neurosci. Methods 25(1):63-74. McGrath, R. A. (1985). Prodesign II: CAD on a budget. Comput. Graphics World 8(12):69-72. McInroy, J. L., and J. J. Capowski (1977). A graphics subroutine package for the neuroscience display

processor. Comput. Graphics 11(1):1-12. McKanna, J. A. (1985). Micros applied to neuroanatomy: Computer-aided morphometry. In: Microcomputers

in the Neurosciences (G. A. Kerkut, ed.). Oxford: Clarendon Press, pp. 152-201. McKanna, J. A., and V. A. Casagrande (1985). Computerized radioautographic grain counting. In: The

Microcomputer in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 356-373.

McKenzie, J. D., Jr., and B. A. Vogt (1976). An instrument for light microscopic analysis of three-dimensional neuronal morphology. Brain Res. 111:411-415.

436 REFERENCES

McMullen, N. T., E. M. Glaser, and M. Tagamets (1984). Morphometry of spine-free nonpyramidal neurons in rabbit auditory cortex. J. Camp. Neurol. 222:383-395.

McMullen, N. T., B. Goldberger, C. M. Suter, and E. M. Glaser (1988). Neonatal deafening alters non­pyramidal dendrite orientation in auditory cortex: A computer microscope study in the rabbit. J. Compo Neurol. 267:92-106.

Mendelsohn, M. L., and B. H. Mayall (1972). Computer-oriented analysis of human chromosomes. III. Focus. Comput. Bioi. Med. 2:137-150.

Mercer, R. R., and J. D. Crapo (1987). Three-dimensional reconstruction ofthe rat acinus. J. Appl. Physiol. 63 (2):785-794.

Mercer, R. R., J. M. Laco, and J. D. Crapo (1987). Three-dimensional reconstruction of alveoli in the rat lung for pressure-volume relationships. J. Appl. Physiol. 62(4):1480-1487.

Miletic, V., and H. J. Tan (1987). Morphology of Golgi-impregnated neurons in the cat and rat nucleus submedius. Soc. Neurosci. Abstr. 13:329.2.

Millar, D. A., and E. D. Williams (1982). A step-wedge standard for the quantification of immunoperoxidase techniques. Histochem. J. 14:609-620.

Miller, J. P., and G. A. Jacobs (1984). Relationships between neuronal structure and function. J. Exp. Bioi. 112:129-145.

Mize, R. R. (1983a). A computer electron microscope plotter for mapping spatial distributions in biological tissues. J. Neurosci. Methods 8:183-195.

Mize, R. R. (1983b). A microcomputer system for measuring neuron properties from digitized images. J. Neurosci. Methods 9: 105-113.

Mize, R. R. (1984). Computer applications in cell and neurobiology: A review. Int. Rev. Cytol. 90:83-124. Mize, R. R. (1985a). Morphometric measurement using a computerized digitizing system. In: The Microcom­

puter in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 177-215. Mize, R. R. (1985b). A microcomputer plotter for use with light and electron microscopes. In: The Microcom­

puter in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 112-133. Mize, R. R. (1985c). Computer applications in neuroscience research. In: Modern Neuroanatomical Methods,

Short Course Syllabus (H. 1. Karten, ed.). Washington, DC: Society for Neuroscience, pp. 94-111. Mize, R. R. (1987). Morphometry of antibody stained cells and synapses using an image analyzer. Neuroscience

[Suppl.] 22:S202. Mize, R. R., and L. H. Horuer (1984). Retinal synapses of the cat medial interlaminar nucleus and ventral

lateral geniculate nucleus differ in size and synaptic organization. J. Compo Neurol. 224:579-590. Mize, R. R., and L. H. Homer (1989). Origin, distribution, and morphology of serotonergic inputs to the cat

superior colliculus: A quantitative light and electron microscope immunocytochemistry study. Exp. Brain Res. 75:83-98.

Mize, R. R., R. F. Spencer, and L. H. Horuer (1986). Quantitative comparison of retinal synapses in the dorsal and ventral parvicellular C, laminae of the cat dorsal lateral geniculate nucleus. J. Compo Neurol. 248:57-73.

Mize, R. R., R. N. Holdefer, and L. B. Nabors (1988). Quantitative immunocytochemistry using an image analyzer. I. Hardware, image processing, and data analysis. J. Neurosci. Methods 26(1):1-23.

Moens, P. B., and T. Moens (1981). Computer measurements and graphics of three-dimensional cellular ultrastructure. J. Ultrastruct. Res. 75:131-141.

Moraff, H. (1976). Laboratory programming: How can we really get it done? In: Computer Technology in Neuroscience (P. B. Brown, ed.). Washington, DC: Hemisphere, pp. 623-648.

Moreton, R. B. (1985). Choosing a microcomputer system. In: Microcomputers in the Neurosciences (G. A. Kerkut, ed.). Oxford: Clarendon Press, pp. 29-89.

Moyer, A., V. Moyer, and P. D. Coleman (1985). An inexpensive PC based system for quantification of neuronal processes. Soc. Neurosci. Abstr. 11:261.18.

Mrzljak, L., H. B. M. Uylings, I. Kostovic, and C. G. Van Eden (1988). Prenatal development of neurons in the human prefrontal cortex: I. A qualitative Golgi study. J. Compo Neurol. 271:355-386.

Mungai, 1. M. (1967). Dendritic patterns in the somatic sensory cortex of the cat, J. Anal. 101:403-418. Nabors, L. B., E. Songu-Mize, and R. R. Mize (1988). Quantitative immunocytochemistry using an image

analyzer. II. Concentration standards for transmitter immunocytochemistry. J. Neurosci. Methods 26:25-34.

Nelson, A. C. (1986). Computer-aided microtomography with true 3-D display in electron microscopy. J. Histochem. Cytochem. 34(1):57-60.

REFERENCES 437

Nierzwicki-Bauer, S. A., D. L. Balkwill, and S. E. Stevens, Ir. (1983). Use of a computer-aided reconstruction system to examine the three-dimensional architecture of cyanobacteria. J. Ultrastruc. Res. 84:73-82.

Norman, D. A. (1981). The trouble with UNIX. Datamations 27:(12):139. Odhner, N. (1911). Eine neue graphische Methode zur Rekonstruktion von Schnittserien in schrager Stellung.

Anat. Anz. 39:273-281. Overdijk, I., H. B. M. Uylings, K. Kuypers, and A. W. Kamstra (1978). An economical, semi-automtic system

for measuring cellular tree structures in three dimensions, with special emphasis on Golgi-impregnated neurons. J. Microsc. 114(3):271-284.

Palacios,1. M., D. L. Niehoff, and M. I. Kuhar (1981). Receptor autoradiography with tritium-sensitive film: Potential for computerized densitometry. Neurosci. Lett. 25:101-105.

Paldino, A. M. (1979). A novel version of the computer microscope for the quantitative analysis of biological structures: Application to neuronal morphology. Comput. Biomed. Res. 12:413-431.

Paldino, A., and E. Harth (1977a). A measuring system for analyzing neuronal fiber structure. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 59-71.

Paldino, A., and E. Harth (l977b). A computerized study of Golgi-impregnated axons in rat visual cortex. In: Computer Analysis of Neuronal Structures (R. D. Lindsay, ed.). New York: Plenum Press, pp. 189-207.

Park, D. (1985). Does Horton's law of branch length apply to open branching systems? J. Theor. BioI. 112: 299-313.

Pamavelas, J. G., and H. B. M. Uylings (1980). The growth of non-pyramidal neurons in the visual cortex of the rat: A morphometric study. Brain Res. 193:373-382.

Patterson, H. A., W. B. Warr, and A. I. Kleinman (1976). A mapping device for attachment to the light microscope. Technical note. Brain Res. 102:323-328.

Pavlidis, T. (1982). Algorithmsfor Graphics and Image Processing. Rockville, MD: Computer Science Press. Pearlstein, R. A., and R. L. Sidman (1986). Computer graphics presentation modes for biologic data. Anal.

Quant. Cytol. Histol. 8(2):89-95. Pearson, 1. c., 1. R. Norris, and C. H. Phelps (1985). Subclassification of neurons in the subthalamic nucleus of

the lesser bushbaby Galago senegulensis: A quantitative Golgi study using principal components analysis. J. Compo Neurol. 238:323-339.

Percheron, G. (1979). Quantitative analysis of dendritic branching. 1. Simple formulae for the quantitative analysis of dendritic branching. Neurosci. Lett. 14:287-293.

Perkins, W. J., and R. J. Green (1982). Three-dimensional reconstruction of biological sections. J. Biomed. Eng. 4:37-43.

Poler, S. M., S. Akeson, and D. G. Flaming (1985). Selection of hardware and software for laboratory microcomputers. In: The Microcomputer in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 47-82.

Pool, C. W., S. Madlener, P. C. Diegenbach, A. A. Sluiter, and P. Van der Sluis (1984). Quantification of antiserum retivity in immunocytochemistry: Two new methods for measuring peroxidase activity on anti­gen-coupled beads incubated according to an immunocytoperoxidase method. J. Histochem. Cytochem. 32: 921-928.

Porath, J., R. Axen, and S. Emback (1967). Chemical coupling of proteins to agarose. Nuture 215:1491-1492. Pratt, W. K. (1978). Digital Image Processing. New York: Plenum Press. Prentice, M. 1. (1978). On invariant tests of uniformity for directions and orientations. Ann. Stat. 6:169-176. Prothero, J. S., and J. W. Prothero (1982). Three-dimensional reconstruction from serial sections. 1. A portable

microcomputer-based software package in FORTRAN. Comput. Biomed. Res. 15:598-604. Prothero, J. S., and J. W. Prothero (1986). Three-dimensional reconstruction from serial sections IV. The

reassembly problem. Comput. Biomed. Res. 19:361-373. Prothero, J. W., A. Tamarin, and R. Pickering (1973). Morphometrics of living specimens. A methodology for

the quantitative three-dimensional study of growing microscopic embryos. J. Microscp. 101(1):31-58. Prothero, 1. S., M. Riggins, A. Lindsay, R. Harris, and J. W. Prothero (1985). Three-dimensional reconstruc­

tion from serial sections. III. AUTOSCAN, a software package in FORTRAN for semi automated pho­tomicrography. Comput. Blomed. Res. 18:132-136.

Pullen, A. H. (1982). A structured program in BASIC for the analysis of peripheral nerve morphometry. J. Neurosci. Methods 5:103-120.

Purves, D., and J. W. Lichtman (1985). Geometrical differences among homologous neurons in mammals. Science 228:298-302.

Putnam, B. W. (1987). RS-232 Simplified. Englewood Cliffs, NJ: Prentice-Hall.

438 REFERENCES

Radermacher, M., and J. Frank (1983). Representation of three-dimensionally reconstructed objects in electron microscopy by surfaces of equal density. J. Microsc. 136(1):77-85.

Radermacher, M., T. Wagenknecht, A. Verschoor, and J. Frank (1987a). Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 146(2):1l3-136.

Radermacher, M., T. Wagenknecht, A. Verschoor, and J. Frank (1987b). Three-dimensional structure of the large ribosomal subunit from Escherichia coli. EMBO J. 6(4): I 107-11 14.

Rakic, P., L. J. Stensas, E. P. Sayre, and R. L. Sidman (1974). Computer-aided three-dimensional reconstruc­tion and quantitative analysis of cells from serial electron microscopic montages of foetal monkey brain. Nature 250:31-34.

Rail, W. (1959). Branching dendritic trees and motorneurons membrane resistivity. Exp. Neural. 1:491-527. Rail, W. (1977). Core conductor theory and cable properties of neurons, In: Handbook of Physiology, Section I:

The Nervous System, Vol. 1, part 1 (J. M. Brookhart and V. B. Mountcastle, Section eds.; E. R. Kandel, Vol. ed.). Bethesda: American Physiological Society, pp. 39-97.

Ramm, P., and J. H. Kulick (1985). Principles of computer-assisted imaging in autoradiographic densitometry. In: The Microcomputer in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 311-334.

Ramm, P., J. H. Kulick, M. P. Stryker, and B. J. Frost (1984). Video and scanning micordensitometer-based imaging systems in autoradiographic densitometry. J. Neurosci. Methods 11:89-100.

Reddy, D. R., W. J. Davis, R. B. Ohlander, and D. J. Bihary (1973). Computer analysis of neuronal structure. In: Intracellular Staining in Neurobiology (S. B. Kater and C. Nicholson, eds.). New York: Springer­Verlag, pp. 227-253.

Reed, D. J., R. Gold, and D. R. Humphrey (1980). A simple computerized system for plotting the locations of cells of specified sizes in a histological section. Neurosci. Lett. 20:233-236.

Reis, D. J., R. H. Benno, L. W. Tucker, and T. H. Joh (1982). Quantitative immunocytochemistry of tyrosine hydroxylase in brain. In: Cytochemical Methods in Neuroanatomy (V. Chan-Palay and S. L. Palay, eds.). New York: Alan R. Liss, pp. 205-228.

Rethelyi, M. (1981). The modular construction of the neuropil in the substantia gelatinosa of the cat's spinal cord. A computer aided analysis of Golgi-specimens. Acta Morphol. Acad. Sci. Hung. 29(1):1-18.

Rethelyi, M., and J. J. Capowski (1977). The terminal arborization pattern of primary afferent fibers in the substantia gelationosa of the spinal cord in the cat. J. Physiol. (Paris) 73:269-277.

Reuman, S. R., and J. J. Capowski (1984). Automated neuron tracing using the Marr-Hildreth zerocrossing technique. Comput. Biomed. Res. 17:93-115.

Ritz, L. A., and J. D. Greenspan (1985). Morphological features of lamina V neurons receiving nociceptive input in cat sacrocaudal spinal cord. J. Camp. Neural. 238:440-452.

Rodieck, R. W., K. F. Binmoeller, and J. Dineen (1985). Parasol and midget ganglion cells ofthe human retina. J. Camp. Neural. 233:115-132.

Rogers, W. T. (1986). Digital microscopy for neurobiology research. College Report, The DuPont Company Sept/Oct.

Rose, P. K., S. A. Kierstead, and S. J. Vanner (1985). A quantitative analysis of the geometry of cat motoneurons innervating neck and shoulder muscles. J. Camp. Neural. 239:89-107.

Rose, R. D., and D. Rohrlich (1987). Counting sectioned cells via mathematical reconstruction. J. Camp. Neural. 263:365-386.

Rosenfeld, A., and A. C. Kak (1982). Digital Image Processing, 2nd ed. New York: Academic Press. Rosenthal, B. M., and W. L. R. Cruce (1984). Contralateral motoneuron dendritic changes induced by transec­

tion of frog spinal nerves. Exp. Neurol. 85:565-573. Rosenthal, B. M., and W. L. R. Cruce (1985). The dendritic extent of motoneurons in frog brachial spinal cord:

A computer reconstruction of HRP-filled cells. Brain Behav. Evol. 27: 106-114. Royer, S. M., and J. C. Kinnamon (1988). Ultrastructure of mouse foliate taste buds: Synaptic and nonsynaptic

interactions between taste cells and nerve fibers. J. Camp. Neural. 270: 11-24. Ruigrok, T. J. H., A. Crowe, and H. J. Ten Donkelaar (1985). Dendrite distribution of identified motoneurons

in the lumbar spinal cord of the turtle Pseudemys scripta elegans. J. Camp. Neural. 238:275-285. Ruiz-Marcos, A. (1983). Mathematical models of cortical structures and their application to the study of

pathological conditions. In: Ramon y Cajal's Contribution to the Neurosciences (S. Grisolia, C. Guerri, F. Samson, S. Norton, and F. Reinoso-Suarez, eds.). Amsterdam: Elsevier, pp. 209-222.

REFERENCES 439

Ruiz-Marcos, A., and S. L. Ipina (1986). Hypothyroidism affects preferentially the dendritic densities on the more superficial region of pyramidal neurons of the rat cerebral cortex. Dev. Brain Res. 28:259~262.

Ruiz-Marcos, A., and F. Valverde (1970). Dynamic architecture of the visual cortex. Brain Res. 19:25-39.

Sadler, M., and M. Berry (1983). Morphometric study of the development of Purkinje cell dendritic trees in the mouse using vertex analysis. 1. Microsc. (O:{[.) 131:341-354.

Sasaki, S., J. K. Stevens, and N. Bodick (1983). Serial reconstruction of microtubular arrays within dendrites of the cat retinal ganglion cell: The cytoskeleton of a vertebrate dendrite. Brain Res. 259: 193-206.

Schall, J. D., and A. G. Leventhal (1987). Relationships between ganglion cell dendritic structure and retinal topography in the cat. 1. Compo Neurol. 257:149-159.

Schipper, J., and F. J. H. Tilders (1983). A new technique for studying specificity of immunocytochemical procedures: Specificity of serotonin immunostaining. 1. Histochem. Cytochem. 31:12-18.

Schipper, J., T. R. Werkman, and F. J. H. Tilders (1984). Quantitative immunocytochemistry of corticotropin­releasing factor CRF: Studies on nonbiological models and on hypothalamic tissues of rats after hypo­physectomy, adrenalectomy and dexamethasone treatment. Brain Res. 293:111-118.

Schwaber, J. S., W. T. Rogers, K. Satoh, and H. C. Fibiger (1987). Distribution and organization of cho­linergic neurons in the rat forebrain demonstrated by computer-aided data acquisition and three-dimensional reconstruction. 1. Compo Neurol. 263:309-325.

Sedivec, M. J., J. J. Capowski, J. Ovelmen-Levitt, and L. M. Mendell (1982). Changes in dendritic organiza­tion of spinocervical tract neurons following partial chronic deafferentation. Soc. Neurosci. Abstr. 8:217.1.

Sedivec, M. J., J. J. Capowski, and L. M. Mendell (1986). Morphology of HRP-injected spinocervical tract neurons: Effect of dorsal rhizotomy. 1. Neurosci. 6(3):661-672.

Seldon, H. L., and D. G. Von Keyserlingk (1978). Preferential orientations of nerve processes in cat and monkey cortex. 1. Anat. 126:65-86.

Shantz, M. J. (1976). A minicomputer-based image analysis system. In: Computer Technology in Neuroscience (P. B. Brown, ed.). Washington, DC: Hemisphere, pp. 113-129.

Shantz, M. J. (1980). Human cortex reconstruction modeled with 70,000 polygons (30,000 polygon portion). Slide 42 of the 1979 Core System Slide Set. Comput. Graphics 13(4):242-246.

Shantz, M. J., and G. D. McCann (1978). Computational morphology: Three-dimensional computer graphics for electron microscopy. IEEE Trans. Biomed. Eng. 25:99-103.

Shay, J. (1975). Economy of effort in electron microscope morphometry. Am. 1. Pathol. 81:503-512. Shneiderrnan, B. (1987). Designing the User Intetface: Strategies for Effective Human-Computer Interaction.

Reading, MA: Addison-Wesley. Sholl, D. A. (1953). Dendritic organization in the neurons of the visual and motor cortices of the cat. 1. Anat.

87:387-406. Sholl, D. A. (1956). The Organization of the Cerebral Cortex. London: John Wiley & Sons. Shreve, R. L. (1966). Statistical law of stream numbers. 1. Geol. 74:17-37. SIGGRAPH (1983). Conference proceedings. Comput. Graphics 17(3):i. Simons, D. J., and T. A. Woolsey (1984). Morphology of Golgi-Cox-impregnated barrel neurons in rat SIP]

cortex. 1. Compo Neurol. 230:119-132. Sing, R. L. A., and E. D. Salin (1985). Programming languages for the laboratory. In: The Microcomputer in

Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 25-45. Sinha, U. K., L. I. Terr, F. R. Galey, and F. H. Linthicum (1987). Computer-aided three-dimensional

reconstruction of the cochlear nerve root. Arch. Otolaryngol. Head Neck Surg. 113:651-655. Sivapragasam, S., J. G. Clement, and E. Dykes (1982). A three-dimensional assessment of dental asymmetry in

human maxillary first premolar teeth. Acta Stereol. 82:297-304. Slepecky, N., H. Larsen, and C. Angelborg (1984). Computerized reconstruction of the regional blood flow in

the rodent cochlea. Hearing Res. 15:95-101. Smart, J. S. (1969). Topological properties of channel networks. Bull. Geol. Soc. Am. 80:1757-1774. Smit, G. J., and H. B. M. Uylings (1975). The morphometry of the branching pattern in dendrites of the visual

cortex pyramidal cells. Brain Res. 87:41-53. Smit, G. J., H. B. M. Uylings, and L. Veldmaat-Wansink (1972). The branching pattern in dendrites of cortical

neurons. Acta Morphol. Neerl. Scand. 9:253-274. Smith, R. G. (1987). MONTAGE: A system for three-dimensional reconstruction by personal computer. 1.

Neurosci. Methods 21:55-69.

440 REFERENCES

Sobel, I., C. Levinthal, and E. R. Macagno (1980). Special techniques for the automatic computer reconstruc­tion of neuronal structures. Annu. Rev. Biophys. Bioeng. 9:347-362.

Sokal, R. R., and F. J. Rohlf (1981). Biometry, 2nd ed. San Francisco: W. H. Freeman. Somogyi, 1., 1. J. Capowski, F. Zsuppan, and L. Dobransky (1987). Data collecting computer terminal for 3D

stick model reconstruction of neuronal structure. Neurosci. 22(suppl):S378. Spacek, J., and M. Hartmann (1983). Three-dimensional analysis of dendritic spines. Anat. Embryol. 167:289-

310. Spacek, 1., and A. R. Lieberman (1974). Ultrastructure and three-dimensional organization of synaptic

glomeruli in rat somatosensory thalamus. J. Anat. 117(3):487-516. Speck, P. T., and N. J. Strausfeld (1983). Portraying the third dimension in neuroanatomy. In: Functional

Neuroanatomy (N. 1. Strausfeld, ed.). Berlin: Springer-Verlag, pp. 156-182. Steffen, H., and H. Van der Loos (1980). Early lesions of mouse vibrissal follicles: their influence on dendrite

orientation in the cortical barrelfield. Exp. Brain Res. 40:419-431. Stephens, M. A. (1964). The testing of unit vectors for randomness. J. Am. Stat. Assoc. 59:160-167. Stephens, M. A. (1966). Statistics connected with the uniform distribution: Percentage points and application to

testing for randomness of directions. Biometrika 53:235-240. Stephens, M. A. (1969). Multi-sample tests for the Fisher distribution for directions. Biometrika 56:169-181. Sternberger, L. A. (1979). Immunocytochemistry, 2nd ed. New York: John Wiley & Sons. Stevens, C. F., and A. N. Van den Pol (1982). Appendix to Van den Pol and Cassidy (1982). J. Compo Neurol.

204:65-98. Stevens, J. K., and 1. Trogadis (1984). Computer-assisted reconstruction from serial electron micrographs: A

tool for the systematic study of neuronal form and function. Adv. Cell. Neurobiol. 5:341-369. Stevens, J. K., T. L. Davis, N. Friedman, and P. Sterling (1980a). A systematic approach to reconstructing

microcircuitry by electron microscopy of serial sections. Brain Res. Rev. 2:265-293. Stevens, 1. K., B. A. McGuire, and P. Sterling (1980b). Toward a functional architecture of the retina: Serial

reconstruction of adjacent ganglion cells. Science 207:317-319. Stevens, J. K., R. Jacobs, and M. L. Jackson (1984). Rings of cross-striated fibrils within the cat cone pedicle:

A computer-assisted serial EM analysis. Invest. Ophtha!. Vis. Sci. 25:201-208. Stevens, J. K., J. Trogadis, and J. R. Jacobs (1988). Development and control of axial neurite form: A serial

electron microscopic analysis. In: Intrinsic Determinants of Neuronal Form and Function (R. J. Lasek and M. M. Black, eds.). New York: Alan R. Liss, pp. 115-145.

Strahler, A. N. (1952). Hypsometric (area-altitude) analysis of erosial topography. Bull. Geol. Soc. Am. 63: 1117-1142.

Streefkerk, J. G., and A. M. Deelder (1975). Serodiagnostic application of immunohistoperoxidase reactions on antigen-coupled agarose beards. J. Immunoglobul. Methods 7:225-236.

Streefkerk, J. G., and M. van der Ploeg (1973). Quantitative aspects of cytochemical peroxidase procedures investigated in a model system. J. Histochem. Cytochem. 21:715-722.

Streefkerk, 1. G., M. van der Ploeg, and P. van Duijn (1975). Agarose beads as matrices for proteins in cytophotometric investigations of immunohistoperoxidase procedures. J. Histochem. Cytochem. 23:243-250.

Street, C. H., and R. R. Mize (1983). A simple microcomputer-based three-dimensional serial section recon­struction system (MICROS). J. Neurosci. Methods 7:359-375.

Street, C. H., and R. R. Mize (1985). An algorithm for removing hidden lines in serial section reconstructions using MICROS. In: The Microcomputer in Cell and Neurobiology Research (R. R. Mize, ed.). New York: Elsevier, pp. 293-308.

Sugiura, Y., E. Schrank, and E. R. Perl (1985). Central ternlinal distribution of unmyelinated afferent fibers. Soc. Neurosci. Abstr. 11:35.6.

Sugiura, Y., C. L. Lee, and E. R. Perl (1986). Central projections of identified, unmyelinated (C) afferent fibers innervating mammalian skin. Science 234:358-361.

Sundsten, J. W., and J. W. Prothero (1983). Three-dimensional reconstruction from serial sections: II. A microcomputer-based facility for rapid data collection. Allat. Rec. 207:665-671.

Sutherland, I. E. (1965). SKETCHPAD: A Man-Machine Graphical Communication System. Cambridge, MA: MIT Lincoln Lab. Abridged version Baltimore: Spartan Books.

Sutherland, I. E., R. F. Sproull, and R. A. Schumacker (1974). A characterization of ten hidden-surface algorithms. Comput. Surv. 6:1-55.

Tamamaki, N., K. Abe, and Y. Nojyo (1988). Three-dimensional analysis of the whole axonal arbors originat-

REFERENCES 441

ing from single CA2 pyramidal neurons in the rat hippocampus with the aid of a computer graphic technique. Brain Res. 452:255-272.

Tayrien, M. W., and R. Loy (1984). Computer-assisted image analysis to quantify regional and specific ligand binding: Up regulation of [3H]QNB and [3H]WB4101 binding in denervated hippocampus. Brain Res. Bull. 13:743-750.

Ten Hoopen, M., and H. A. Reuver (1970). Probabilistic analysis of dendritic branching patterns of cortical neurons. Kybernetik 6:176-188.

Thompson, R. P., Y. M. Wong, and T. F. Fitzharris (1983). A computer graphic study of cardiac truncal septation. Anat. Rec. 206:207-214.

Tieman, D. G., and R. K. Murphey (1985). A computer-assisted video technique for preparing pictures of intracellularly filled, whole-mounted neurons in the cricket. Soc. Neurosci. Abstr. 11:184.5.

Tieman, D. G., R. K. Murphey, 1. T. Schmidt, and S. B. Tieman (1986). A computer-assisted video technique for preparing high resolution pictures and sterograms from thick specimens. J. Neurosci. Methods 17:231-245.

Tieman, S. B., and H. V. B. Hirsch (1982). Exposure to lines of only one orientation modifies dendritic morphology of cells in the visual cortex of the cat. J. Compo Neurol. 211:353-362.

Toga, A. W., and T. L. Arnicar (1985). Image analysis of brain physiology. Comput. Graph. Appl. 5:20-25. Toga, A. W., and T. L. Arnicar-Sulze (1987). Digital image reconstruction for the study of brain structure and

function. J. Neurosci. Methods 20:7-21. Tolivia, I., D. Tolivia, and M. Alvarez-Uria (1986). A three-dimensional reconstruction program for personal

computers. J. Neurosci. Methods 17:55-62. Tombol, T., M. Madarasz, and 1. Martos (1983). Quantitative aspects in the analysis of the synaptic architecture

of thalamic sensory relay nuclei. Acta Bioi. Hung. 34(2-3):275-301. Triller, A., and H. Korn (1986). Variability of axonal arborizations hides simple rules of construction: A

topological study from HRP intracellular injections. J. Compo Neurol. 253:500-513. Tumosa, N., S. B. Tieman, and D. G. Tieman (1989). Binocular competition affects the patter and intensity of

ocular activation columns in the visual cortex of cats. Vis. Neurosci. (in press). Ulfhake, B., and 1.-0. Kellerth (1981). A quantitative light microscopic study of the dendrites of cat spinal (X­

motoneurons after intracellular staining with HRP. J. Compo Neurol. 202:571-584. Unnerstall, J. R., D. L. Niehoff, M. J. Kuhar, and J. M. Palacios (1982). Quantitative receptor autoradiography

using [3H]Ultrofilm: Application to multiple benzodiazepine receptors. J. Neurosci. Methods 6:59-73. Upfold, J. B., M. S. R. Smith, and M. J. Edwards (1987). Three-dimensional reconstruction of tissue using

computer-generated images. J. Neurosci. Methods 20:131-138. Usson, Y., S. Torch, and G. Douret d' Aubigny (1987). A method for automatic classification of large and small

myelinated fibre populations in peripheral nerves. J. Neurosci. Methods 20:237-248. Uylings, H. B. M., and H. K. P. Feirabend (1983). Golgi staining methods, In: Manual of Neuroanatomical

Staining Methods (H. B. M. Uylings, E. Marani, A. H. M. Lohman, and G. Vrensen, eds.). Amsterdam: Netherlands Neuroanatomists Verhaart Meetings Publication, pp. 9.1-9.42 (in Dutch).

Uylings, H. B. M., and G. 1. Smit (1975). Three-dimensional branching structure of pyramidal cell dendrites. Brain Res. 87:55-60.

Uylings, H. B. M., G. J. Smit, and W. A. M. Veltman (1975). Ordering methods in quantitative analysis of branching structures of dendritic trees. Adv. Neurol. 12:247-254.

Uylings, H. B. M., K. Kuypers, M. C. Diamond, and W. A. M. Veltman (1978a). Effects of differential environment on plasticity of dendrites of cortical pyramidal neurons in adult rats. Exp. Neurol. 62:658-677.

Uylings, H. B. M., K. Kuypers, and W. A. M. Veltman (1978b). Environmental influences on neocortex in later life. In: Maturation of the Nervous System, Progress in Brain Research, Vol. 48 (M. A. Comer, R. E. Baker, N. E. van de Poll, D. F. Swaab, and H. B. M. Uylings, eds.). Amsterdam: Elsevier, pp. 261-274.

Uylings, H. B. M., J. G. Parnavelas, H. Walg, and W. A. M. Veltman (1980). The morphometry of the branching pattern of developing non-pyramidal neurons in the visual cortex of rats. Mikroskopie 37(Suppl.):220-224.

Uylings, H. B. M., R. W. H. Verwer, J. van Pelt, and 1. G. Parnavelas (1983). Topological analysis of dendritic growth at various stages of cerebral development. Acta Stereol. 2(1):55-62.

Uylings, H. B. M., A. Ruiz-Marcos, and J. van Pelt (1986a). The metric analysis ofthree-dimensional dendritic tree patterns: A methodological review. J. Neurosci. Methods 18:127-151.

Uylings, H. B. M., C. G. Van Eden, and M. A. Hofman (l986b). Morphometry of size/volume variables and

442 REFERENCES

comparison of their bivariate relations in the nervous system under different conditions. J. Neurosci. Methods 18:19-37.

Uylings, H. B. M., M. A. Hofman, and M. A. H. Matthijssen (1987). Comparison of bivariate linear relations in biological allometry research. Acta Stereo!' 6(Suppl. III):467-472.

Valverde, F. (1970). The Golgi method. A tool for comparative structural analyses. In: Contemporary Research Methods in Neuroanatomy ('N. 1. H. Nauta and S. O. E. Ebbeson, eds.). Berlin: Springer-Verlag, pp. 12-31.

Van Dalen, 1. P. R., W. Knapp, and J. S. Ploem (1973). Microfluorometry on antigen-antibody interaction in immunofluorescence using antigens covalently bound to agarose beads. J. Immunol. Methods 2:383-392.

Van den Pol, A. N., and J. R. Cassidy (1982). The hypothalamic arcuate nucleus of the rat-a quantitative Golgi analysis. J. Compo Neurol. 204:65-98.

Van der Loos, H. (1959). [Dendro-dendritic Connections in the Cerebral Cortex.] Doctoral dissertation, University of Amsterdam (in Dutch).

Vandesande, F. (1979). A critical review of immunocytochemical methods for light microscopy. J. Neurosci. Methods 1:3-23.

Van Duijn, P., E. Pascoe, and M. van der Ploeg (1967). Theoretical and experimental aspects of enzyme determination in a cytochemical model system of polyacrylamide films containing alkaline phosphatase. J. Histochem. Cytochem. 15:631-645.

Van Pelt, J., and R. W. H. Verwer (1983). The exact probabilities of branching patterns under terminal and segmental growth hypothesis. Bull. Math. BioI. 45:269-285.

Van Pelt, J., and R. W. H. Verwer (l984a). New classification methods of branching patterns, J. Microsc. (0:4'.) 136:23-34.

Van Pelt, J., and R. W. H. Verwer (l984b). Cut trees in the topological analysis of branching patterns. Bull. Math. BioI. 46:283-294.

Van Pelt, 1., and R. W. H. Verwer (1985). Growth models (including terminal and segmental branching) for topological binary trees. Bull. Math. BioI. 47:323-336.

Van Pelt, J., and R. W. H. Verwer (1986). Topological properties of binary trees grown with order-dependent branching probabilities. Bull. Math. BioI. 48:197-211.

Van Pelt, J., and R. W. H. Verwer (1987). Mean centrifugal order as a measure for branching pattern topology. Acta Stereol.6:393-397.

Van Pelt, 1., R. W. H. Verwer, and H. B. M. Uylings (1986). Application of growth models to the topology of neuronal branching patterns. J. Neurosci. Methods 18:153-165.

Vaughn, J. E., R. P. Barber, and T. J. Sims (1988). Dendritic development and preferential growth into synaptogenic fields: A quantitative study of Golgi-impregnated spinal motor neurons. Synapse 2:69-78.

Veen, A., and L. D. Peachey (1977). TROTS: A computer graphics system for three-dimensional reconstruction from serial sections. Comput. Graphics 2:135-150.

Verwer, R. W. H., and J. van Pelt (1983). A new method for the topological analysis of neuronal tree structures. J. Neurosci. Methods 8:335-351.

Verwer, R. W. H., and 1. Van Pelt (1985). Topological analysis of binary tree structures when occasional multifurcations occur. Bull. Math. BioI. 47:305-316.

Verwer, R. W. H., and J. Van Pelt (1986). Descriptive and comparative analysis of geometrical properties of neuronal tree structures. J. Neurosci. Methods 18:179-206.

Verwer, R. W. H., and J. Van Pelt (1987). Multifurcations in topological trees: Growth models and comparative analysis. Acta Stereol. 6:399-404.

Verwer, R. W. H., J. Van Pelt, and H. B. M. Uylings (1985). A simple statistical test for the vertex ratio using Monte Carlo simulation. J. Neurosci.Methods 14:137-142.

Verwer, R. W. H. J. Van Pelt, and A. J. Noest (1987). Parameter estimation in topological analysis of binary tree structures. Bull. Math. BioI. 49:363-378.

Villa, A. E. P., M. Bruchez, G. M. Simm, and S. Jeandrevin (1987). A computer-aided three-dimensional reconstruction of brain structures using high level computer graphics. Int. J. Biomed. Comput. 20:289-302.

Voyvodic, 1. T. (1987). Development and regulation of dendrites in the rat superior cervical ganglion. J. Neurosci. 7:904-912.

Wallen, P., K. Carlsson, A. Liljeborg, and S. Grillner (1988). Three-dimensional reconstruction of neurons in the lamprey spinal cord in whole-mount, using a confocal laser scaning microscope. J. Neurosci. Methods 24:91-100.

REFERENCES 443

Wann, D. F. (1976). Counting high contrast closed objects in biological images using a 525-line raster scan television camera and a minicomputer. In: Computer Technology in Neuroscience (P. B. Brown, ed.). Washington, DC: Hemisphere, pp. 135-137.

Wann, D. F., T. A. Woolsey, M. L. Dierker, and W. M. Cowan (1973). An on-line digital computer system for the semiautomatic analysis of Golgi-impregnated neurons. IEEE Trans. Biomed. Eng. 20:233-247.

Wann, D. F., J. L. Price, W. M. Cowan, and M. A. Agulnek (1974). An automated system for counting silver grains in autoradiographs. Brain Res. 81:31-58.

Ware, R. W., and V. LoPresti (1975). Three-dimensional reconstruction from serial sections. In: International Review o/Cytology, Vol. 40 (G. H. Bourne and J. F. Danielli, eds.). New York: Academic Press, pp. 325-440.

Waters, J. R., and A. J. Chester (1987). Optimal allocation in multivariate, two-stage sampling designs. Am. Stat. 41:46-50.

Watson, G. S., and E. J. Williams (1956). On the construction of significance tests on the circle and the sphere. Biometrika 43:344-352.

Webb, W. W. (1986). Light microscopy-a modem renaissance. Ann. N.Y. Acad. Sci. 483:387-391. Wegman, E. J., and D. J. DePriest, eds. (1986). Statistical/mage Processing and Graphics. New York: Marcel

Dekker. Weinstein, M., and K. R. Castleman (1971). Reconstructing three-D specimens from two-D section images.

Proc. Soc. Photo-opt. Instrum. Eng. 26:131. Werner, C., and J. S. Smart (1973). Some new methods of to po logic classification of channel networks. Geogr.

Anal. 5:271-295. West, M. 1. (1985). Neuroanatomical modeling with CADCAM. Soc. Neurosci. Abstr. 11:184.6. Willey, T. J., R. L. Schultz, and A. H. Gott (1973). Computer graphics in three dimensions for perspective

reconstruction of brain ultrastructure. IEEE Trans. Biomed. Eng. 20:288-291. Williams, F. G., and R. Elde (1982). A microcomputer-aided system for the graphic reproduction of neu­

rohistochemical maps. Comput. Prog. Biomed. 15:93-102. Williams, R. S., and S. Matthijsse (1983). Morphometric analysis of granule cell dendrites in the mouse dentate

gyrus. J. Compo Neurol. 215:154-164. Williams, R. S., and S. Matthijsse (1986). Age-related changes in Down syndrome brain and the cellular

pathology of Alzheimer disease. Prog. Brain Res. 70:49-67. Wind, G., V. K. Dvorak, and J. A. Dvorak (1986). Computer graphic modeling in surgery. Orthop. Clin. North

Am. 17(4):657-668. Wind, G., R. W. Finley, and N. M. Rich (1988). Three-dimensional computer graphics modeling of ballistic

injuries. J. Trauma 28(1):SI6-S20. Winslow, 1. L., M. Bjerknes, and H. Cheng (1987). Three-dimensional reconstruction of biological objects

using a graphics engine. Comput. Biomed. Res. 20(6):583-602. Woolsey, T. A., and M. L. Dierker (1978). Computer-assisted recording of neuroanatomical data. In:

Neuroanatomical Research Techniques (R. T. Robertson, ed.). New York: Academic Press, pp. 47-85.

Woolsey, T. A., and M. L. Dierker (1982). Morphometric approaches to neuroanatomy with emphasis on computer-assisted techniques. In: Cytochemical Methods in Neuroanatomy (V. Chan-Palay and S. L. Palay, eds.). New York: Alan R. Liss, pp. 69-91.

Yaegashi, H., T. Takahashi, and M. Kawasaki (1987). Microcomputer-aided reconstruction: A system designed for the study of 3-D microstructure in histology and histopathology. J. Microsc. 146(1):55-65.

Yelnik, 1., G. Percheron, J. Perbos, and C. Fran«ois (1981). A computer-aided method for the quantitative analysis of dendritic arborizations reconstructed from several serial sections. J. Neurosci. Methods 4:347-364.

Yelnik, J., G. Percheron, C. Fran«ois, and Y. Burnod (1983). Principal component analysis: A suitable method for the 3-dimensional study of the shape, dimensions and orientation of dendritic arborizations. J. Neuro­sci. Methods 9:115-125.

Yelnik, 1., C. Fran«ois, G. Percheron, and S. Heyner (1987). Golgi study of the primate substantia nigra. I. Quantitative morphoiogy and topology of nigral neurons. J. Compo Neurol. 265:455-472.

Young, S. L., E. K. Fram, and B. L. Craig (1985). Three-dimensional reconstruction and quantitative analysis of rat lung type II cells: a computer-based study. Am. J. Anat. 174:1-14.

Young, S. L., S. Royer, P. M. Groves, and J. C. Kinnamon (1987). Three-dimensional reconstructions from serial micrographs using the IBM Pc. J. Electron Microsc. Tech. 6:207-217.

444 REFERENCES

Zsuppan, F. (1984). A new approach to merging neuronal tree segments traced from serial sections. 1. Neurosci. Methods 10:199-204.

Zsuppan, F. (1985). A computer reconstruction system for biological macro- and microstructures traced from serial sections. Acta Morphol. Hung. 33(1-2):33-44.

Zsuppan, F. (1987). The methodology of entering neuronal structure into a computer. Neurosci. 22(suppl): S393.

Zsuppan, F., and M. Rethelyi (1985). Approximation of missing sections in computer reconstruction of serial EM pictures. 1. Neurosci. Methods 15:203-212.

Selected Reading

BOOKS AND SPECIAL JOURNAL VOLUMES

Bourne, J. R. (1981). Laboratory Minicomputing. New York: Academic Press. Brooks, F. P., Jr. (1975). The Mythical Man-Month. Reading, MA: Addison-Wesley. Brown, P. B., ed. (1976). Computer Technology in Neuroscience. Washington, DC: Hemisphere. Castleman, K. R. (1979). Digital Image Processing. Englewood Cliffs, NJ: Prentice - Hall. Foley, 1. D., and A. van Dam (1982). Fundamentals of Interactive Computer Graphics. Reading, MA:

Addison-Wesley. Fraser, P. J., ed. (1988). Microcomputers in Physiology: A Practical Approach. Oxford: IRL Press. Gage, S. H. (1941). The Microscope. Ithaca, NY: Comstock. Gaunt, P. N., and W. A. Gaunt (1978). Three-Dimensional Reconstruction in Biology. Tunbridge Wells:

Pitman. Gonzales, R. c., and P. W. Wintz (1977). Digital Image Processing. Reading, MA: Addison-Wesley. Inoue, S. (1986). Video Microscopy. New York: Plenum Press. Karshmer, A. I., and M. A. Arbib, eds. (1978). Computers in the Neurosciences. Special issue of the Brain

Theory Newletter 3(3-4). Amherst, MA: Center for Systems Neuroscience. Kerkut, G. A., ed. (1985). Microcomputers in the Neurosciences. Oxford: Clarendon Press. Lasek, R. J., and M. M. Black, eds. (1988). Intrinsic Determinants of Neuronal Form and Function. New

York: Alan R. Liss. Lindsay, R. D., ed. (1977). Computer Analysis of Neuronal Structures. New York: Plenum Press. McEachron, D. (1986). Function Mapping in Biology and Medicine: Computer Assisted Autoradiography.

Basel: Karger. Mize, R. R., ed. (1985). The Microcomputer in Cell and Neurobiology Research. New York: Elsevier. Newman, W. M., and R. F. Sproull (1979). Principles of Interactive Computer Graphics, 2nd ed. New York:

McGraw-HilI. Pratt, W. K. (1978). Digital Image Processing. New York: John Wiley & Sons. Rosenfeld, A., and A. C. Kak (1982). Digital Imaging Processing, 2nd ed. New York: Academic Press. Sholl, D. A. (1956). The Organization of the Cerebral Cortex. London: John Wiley & Sons. Somlyo, A. P., ed. (1986). Recent advances in electron and light optical imaging in biology and medicine. Ann.

N.Y. Acad. Sci. 483:387-391. Uylings, H. B. M. (1977). A Study on Morphometry and Functional Morphology of Branching Structures, with

Applications to Dendrites in Visual Cortex of Adult Rats under Different Environmental Conditions. Amsterdam: Kaal's Printing House.

Uylings, H. B. M., R. W. H. Verwer, and 1. van Pelt, eds. (1988). Morphometry and Stereology ill Neuro­sciences. Special issue of Journal of Neuroscience Methods 18(1-2). Amsterdam: Elsevier.

445

446

PERIODICALS

Computer Applications in the Biosciences. Oxford: IRL Press. Computers in Biology and Medicine. Oxford: Pergamon Press. Computers and Biomedical Research. San Diego: Academic Press. Computers and Medicine. Glencoe, IL: Medical Group News. Computer Methods and Programs in Biomedicine. Amsterdam: Elsevier.

SELECTED READING

IEEE Transactions on Biomedical Engineering. Piscataway, NJ: Institute of Electrical and Electronic Engineers. International Journal of Biomedical Computing. Limerick: Elsevier. Journal of Electrophysiological Techniques. New York: Pergamon Press. Journal of Microscopy. Oxford: Blackwell Scientific Publications. Journal of Neuroscience Methods. Amsterdam: Elsevier. SIGBIO (Special Interest Group on Biomedical Computing). New York: Association for Computing Machinery. SIGCHI (Special Interest Group on Computer-Human Interaction). New York: Association for Computing

Machinery. SIGGRAPH (Special Interest Group on' Computer Graphics). New York: Association for Computing

Machinery.

Index

Note: The suffixes g, f, n, and t denote glossary, figure, footnote, and table, respectively.

5-HT, 371; see also Serotonin (5-HT) 8086, 19, 65 8087, 19, 65 68000, 19, 67 68020,67 80286,65 80287,65 80386,66 80387,66 ABC: see Avidin-biotin complex ADC, 19, 51, 287f AID converter, 42, 334, 337, 338, 338, 343, 366

interface to, 367 used in tracing, 92

AGC, 19,2g ALGOL, 19, 81 ALU, 2g, 44 ANOV A: see Analysis of variance AOD: see Average optical density AOI: see Area, of interest ASCII, 2g, 44, 72

characters, 43, 44 fIles, 2g, 78, 79

advantages and disadvantages, 163 Abbe, E., 28 Abort capability in commands, 268 Absolute positioning, 57 Access time, of disks, 45 Acetylcholinesterase, 371 Acoustic data tablet, 57, 58f ADA, 19, 81 Adapter

C-mount,4g asynchronous: see Asynchronous port color graphics: see CGA enhanced graphics: see EGA Hercules monochrome adapter: see MDA EGA, 8g, 47, 288 MDA, 13g, 14g, 47

Adapter (cont.) MGA, 109, 13g, 47 VGA, 21g, 47, 66, 288

Additive mixing of colors, 302, 303 Address, 19, 45 Adsorption controls, 363 Agar, 364

standards for, 371 Agarose, 364

beads, 364 Airline distance, 195, 195f

from soma, 200 Algebraic clipping, 170f

cost of, 169 Algebraic data base manipulation, 157 Algebraic equations, 77 Algorithm, 19, 72

for noise correction, 341 for shading correction, 339, 340f

Aliasing, problem of, 19, 55, 160, 178, 179, 182; see also Raster, displays

cost of antialiasing, 183 in raster displays, 182,183f techniques for antialiasing, 182

Alignment by image superposition, 119 of serial sections, 119, 154

automatic, history of, 126, 127 computer-assisted, 120 cumulative errors, 119 with pin holes, 120 use of 35-mm slides, 119 using cut tissue edge, 120 using fiducial marks, 120, 155

of video images, 292, 327 All-order partition analysis, 228

of trees, 223, 225, 226f, 238 Ambilateral tree types, 2g, 218n American Innovision, Inc., 387, 388f

447

448

American Standard Code for Information Interchange, 2g, 44; see also ASCII

Amygdala, 370 Analog,2g Analog plotter, 32 Analog-to-digital converter: see AID converter Analog values, 43 Analog video, gain and offset, 297 Analysis, see also Neurons, analysis of

of branch points, 207, 21Of, 246, 247 of immunohistochemical data, 333 of incomplete trees, 217, 236, 237

Analysis of variance, 261 Analytical Imaging Concepts, Inc., 388 Anatomical axes, standard, 200, 201 Anding, mask and image, 142f Anterior commissure, 370 Antialiasing: see Aliasing Antibodies, 347f, 352f, 353f, 356, 357f, 358, 360,

362, 365f, 369, 370, 371 concentration of, 362 dilution of primary, 362 immunocytochemistry with, 333 primary, 363 release of, 370 secondary, 362 storage of, 370 synthesis of, 370 transport of, 370 to tyrosine hydroxylase, 363

Antigen, 333, 334, 363, 364, 365f concentration of, 362, 371

Aperture, 2g Apple Corporation, 66, 67 Apple 11,66 Apple MacIntosh, 4lf, 67,117,273,274 Application software, 74, 78, 265 Application systems, 366 Area

-based measurements, 195 cross-sectional, 195, 196f, 344

of a dendritic field, 196 of interest, 2g of irregular boundary, 356 within a polygon, calculating, 195, 196f of region of interest, 140, 197, 198f range used in cell couting, 144

Arithmetic and logical unit: see ALU Arithmetic operations, 2g, 44 Array,2g

processor, 336 Artificially enriched displays, J 25 Artist's assistant, 28, 32 Aspect ratio, 2g

of television, 288 Assay, biochemical, 333 Assemblers, 2g, 76

language, 76, 77 process of assembling. 2g, 76

Asymmetry of trees, 'measures for, 232 Asynchronous port, 2g, 62

INDEX

Attaching new tree to existing stump, 152, 153f, 154, 156f

Augusta Ada, 81 Author of software, 83 Automatic alignment of sections using video,

history, 147 Automatic cell counting, 144 Automatic data storage, 279 Automatic silver grain counting, 143 Automatic dendrite tracking: see Automatic neuron

tracing Automatic focusing, 144, 144f

history, 147 Automatic gain control: see AGC Automatic neuron tracing, 375, 377f, 378, 379; see

also Neuron tracing algorithms, 376, 377f, 378, 379 using better image enhancement, 381 using bigger computers, 380 computer science research, 380, 386 determining focal plane, 378 further reading, 386 future biological results, 386 future work, 380, 386 hardware for, 376f, 378f history of, 376 locating details, 375, 377f, 378, 379 measuring dendritic thickness, 378 objectivity, computer versus human, 375 operator intervention, 376 pattern recognition in, 35, 87, 132, 158 performance of, 377

compared to a person, 386 use of reflected light microscope, disadvantages,

385 using confocal microscope, 381, 382 using edge-detection algorithms, 381 using faster computers, 380 relations to other sciences, 386 results of, 374f, 377, 379, 380 review of, 386 using spatial filters, 381 state-of-the-art, 375 systems in use, 376 television-based, 377, 378f template matching, 381 using voxel-based image representation, 188,

380, 386 vidissector-based, 376f

Automatic particle counting, 143f history of, 147

Automatic point capturing, 101 Automatic polygon closing, 117 Automatic reconstruction, the problem, 373 Automatic tracing of structures, 132 Automatic tracing using video, history, 147 Autoradiography, 329, 330

quantitative receptor, 367, 368 silver grain counting, 143

Average optical density, 338, 342f. 343, 344f, 362, 365f, 368

INDEX

Avidin-biotin complex, 360 Axes

orthogonality of, 15g of rotation for displays, 168f standard anatomical, 200, 201

Axon Instruments, Inc., 389 Axons

swellings, 36 distribution of, 202f versus branch order, 202f

terminals, 358 synaptic, 360, 36lf

BALB/cJ rats, 370 BASIC, 3g, 80, 80f BIOS, 3g, 75 Background

field, 343 fluctuations of images, 312 image, 339, 340f, 340, 341

corrections cost of, 313 real-time, 313

subtraction, 3g, 329 of programmers, 85

Backup of data, 279 need for, 279

Banking, use of computers in, 81 Basic: see BASIC Basic Input/Output System, 3g, 75 Batch file, 73 Baud, 3g, 62 Baudot, Emile, 3g, 62 Beads, agarose, 364 Beeping, 280 Beginner's all-purpose symbolic instruction code:

see BASIC

Bell Telephone Laboratories, 76 Benchmark, 47 Bending factor of a dendrite, 195, 195f; see also

Tortuosity Bernoulli box, use in storage of images, 295 Bifurcation, 3g, 4g, 99; see also Branchpoint

angle of, 246, 247 types of, 245f

Binary digit: see Bit Binary editing, 356, 358

of an image, 348f, 349f Binary files, advantages and disadvantages, 162 Binary image, 350, 355 Binary image operators, 366 Binary numbers, 3g, 43 Binary operations software, 366, 367 Binary operators, 351 Binary trees, 157, 225, 232

characteristics, 157, 158f storage of, 158f

Biochemical assay, 333 Biochemical techniques, 333 Biographics, Inc., 390, 391f, 392f Bio Image-a Kodak Company, 391, 393f, 394f

Biological utility of image measurements, 369 Biologist's perspective of computers, 86 Bio-Rad, 392, 395f Bipolar color scheme, 304f Bit, 3g, 42 Bit-map graphics, 47 Bit plane, 336, 338, 350 Blooming, 3g, 298, 299f Blur, 3g, 298f

removal by filtering, 322f, 323f, 325f Blurred images, corrections for, 313, 314 Board, see also Card

computer, 3g mother, 14g, 63

Body, weight of, 262 Bookkeeper, 35

using comuters as, 89 BooIe, G, 3g, 44 Boolean operations, 44 Boot; see Bootstrap Bootstrap, 3g, 4g, 74

449

Botanical tree growth versus dendritic tree growth, 214

Bottom artificial end, 98f, 99 Bottom tree origin, 99 Boundary, 354f, 355 Bounded tasks, 67 Bound ligand, 368 Bovine serum albumin, 364 Brain

anterior commissure, 370 lesions of, 370 measurements of, 356 weight of, 262

Brain paste, 364 Branching pattern, 209f

symmetry of, 198 Branch order, 4g, 15g, 95f, 97, 201

centrifugal, 5g, 230f, 235, 236, 245f for apical dendrites, 246f sum of, 228, 230 of a tree, 228 of tree segments, 218f

centripetal, 5g, 230f, 235, 236 Horsfield, 230f, 236 Strahler, 230f, 236 of tree segments, 163, 230f, 235, 236

use in metric analysis, 244, 245 Branchpoint, 4g, 97, 99

analysis of, 207, 21Of, 246, 247 exiting angle of, 4g, 207, 210f daughter angle, 6g daughter fiber, 7 g mother fiber, 14g parent fiber, 15g Rail's ratio, 207, 210f return to from ending during tracing, 134

Branch segments, 4g, 195,201,217 analysis of, 202 lengths, 245

histogram, 205f

450

Brauch segments (cont. ) lengths (cont.)

vs order, 205f, 206, 245 measurements of, 244 tapering of, 206, 207f, 208f, 243 thickness versus order, 206, 206f

Bug,4g, 63, 74 Burleigh Instruments, Inc., 394, 396f Bum-in, 4g, 294 Bus, 4g, 39, 48, 63, 64f

address lines, 48 data lines, 48 hand-shaking lines, 48 IEEE-488, Ilg MCA,66 Nu-bus,67 Q-bus,68 standardization of, 48 width of, 48 Unibus, 68 VME, 22g, 67

Byron, Lord, Ig, 81 Byte, 4g, 43

C, 4g, 76, 79, 80f CADCAM, use in serial section reconstruction, 127 CBA/J rats, 370 CCD, 4g, 5g, 293, 336

arrays, 293 time required to scan, 293

CCIR, 4g, 288 CCTV, 4g, 5g CD: see Compact disks, use in storage CFF: see Critical flicker frequency CGA, 2g, 5g, 47, 288; see also Color graphics

adapter cm, 336 COBOL, 5g, 81 CPU, 5g, 6g, 40, 44, 336

68000, Ig, 67 68020,67 8086, Ig, 65 80286,65 80386,66 Z-80,66

CRT,4g, 6g, 52, 52f blooming of, 3g, 298, 299f displays on, 165 electron beam, 52 electron gun, 8g phosphor, 16g, 53

persistence of, 16g, 177 yoke,22g

Cable properties of neurons, 214 Cage, card, 65

slot in, 199 Cajal, S. R. Y., 23, 24f, 28 Calibration of the data tablet, 114, 277 Calibration of electron microscope, 337 Camera lucida, 28, 29f, 3If

disadvantages of, 31 drawing with, 30f, 29f, 31

Camera lucida (cont.) drawing tube, 31 use with microscope, 29 use in serial section reconstruction, 113 use during tracing, 91, 1l6f

Camera, television: see Television, camera Capacity of memory, 13g Carbon grating replica, 337 Card, 4g; see also Board Card cage, 65

slot in, 199

INDEX

Cartesian grid analysis of dendritic orientation, 254, 255, 256f

Castration, 370, 371 Catalog of files, 75; see also Directory of files Catecholamines, 333 Cathode ray tube: see CRT Cells, see also Neurons

clumps of, 143f counting of, 143, 143f

automatic, 144 form factor, 196f, 197,344,355

calculation of, 196 geometry, measurements of, 368 histogram of sizes, 359f imaging of, 368 measured by image analyzer, 356, 358; see also

Neurons, measurements of measurements of, 356, 358

area, 358, 366 breadth, 366 cross-sectional area, 36lf length, 36lf, 366 optical density, 358, 366 perimeter, 358, 36lf shape factor of, 344, 355

segmentation of, 358 Center of dendritic length, 198 Center of gravity, 198 Center of neuron, measurement of, 198 Center of surface area, 199 Central processing unit, see CPU Centrifugal order, 5g, 230f, 235, 236, 245f

for apical dendrites, 246f use in metric analysis, 244, 245 sum of, 228, 230 of a tree, 228 of tree segments, 218f

Centripetal order, 5g, 230f, 235, 236 Centroid of a dendritic field, 253, 254f Centronics port, 62 Chalnicon tube, 293 Characters, 43, 44; see also ASCII

EBCDIC,8g Charge-coupled devices: see CCD Charge-injection diode, 336 Chip, 5g, 63; see also Integrated circuit Chi-square test, 221

for dendritic orientation, 252 for topological parameters, 238

Chord length, 355 Chromagen, 347f, 360

INDEX

Chromaticity diagram, 303 Cingulate cortex, 371 Circular cursor in microscope, 95f, l06f Circumscribing a neuron by a polygon, 198f Classification of tree types, 217, 220t, 221, 222f

by class number, 219 by PSAD values, 225

Clicking a mouse, 269, 272f Clipping, 169, 169f

algebraic, 170f cost of, 169

of dynamic displays, 169 in serial section reconstruction, 188f of voxels, 188, 188f to reveal inner portions of structures, 170

Clock speeds, 47 Clone, 5g, 65, 66, 68

accessories for, 69 companies that manufacture, 69 purchasing of, 69

Closed-circuit television, 4g, 5g Closed-loop system, 5g Closed polygons during mapping, 101 Close point, 122 Closing operation on images, 5g, 311, 311f, 351,

356 Closure, principle of in programming, 268 Clumps of cells, 143f Clustering of points, 213, 213f

Poisson distribution of, 213 C-mount adapter, 4g Code, 71; see also Program Coding, Ig, 5g Coefficient of variation, 259 Color

bipolar scheme of, 304f filters, 146 hue, Ilg image processing using a monochrome camera, 295 information loss with video, 146 intensity, 303 mixing

additively, 302, 303 subtractively, 302, 303

palette, 15g, 288 plots using, 190 primary, 287f, 302, 303, 303f saturation, 303 space, 303, 303f, 304f use during tracing, 119

Color graphics adapter, 5g, 288; see also CGA Combining images, 326

arithmetic operators for, 336 by image processing, 327, 328f, 329, 329f image subtraction, 329 reflected- and transmitted-light confocal images,

385, 385f Command,5g Command file, 73 Command language, 5g Command-line interface, 271, 272

advantages and disadvantages of, 273

Command-line interface (cant.) programmable, 273 programmer's viewpoint, 273

Command operands, 275 Command selection of a program, 268 Commercially available computer systems for

neuroanatomy, 387

451

Common business-oriented language, 81; see also COBOL

Communication, asynchronous, 2g Compact disks, use in data storage, 296 Compaq Corporation, 66 Compass heading, 198f Compatibility, 5g, 69

upward,21g Compiler, 5g, 72, 77 Component systems, 366 Components of variance in statistical tests, 258,

26O,26lt Composite video, 6g, 53 Computations on the data base to overcome

hardware constraints, 163 Computer-aided design, computer-aided

manufacturing: see CADCAM Computer-driven return to branchpoint, 98, 98f; see

also Neuron tracing Computer-generated overlay for merging, 152, 153f Computer-generated overlay in microscope, 98 Computer graphics, see also Displays

algorithms for displays, review of, 192 coordinate systems for, 168, 168f depth cues, 167

hidden-line and -surface removal, 173, 173f, 174f

intensity variation, 173 value of, 173

smooth rotation, 178 stereo pairs, 175, 176, 176f

use in flight simulation, 171 history of, 191

Sketchpad, 165 in neuroanatomy

history of, 191 special probems, 191

textbooks, 192 use for presenting program output, 281

Computer program, 71; see also Program; Software Computer representation of traced data, 95 Computers

applications in neuroanatomy, review of, 371 use in banking, 81 biologist's perspective of, 86 as bookkeepers, 89 compatibility, 5g, 69

upward,21g components of, 41f, 39 to control microscope focus, 145 economics of, 82, see also Economics of

computing justification for, 375 laboratory

80386 machines, 66

452

Computers (cont.) laboratory (cont. )

Apple II, 66 Apple MacIntosh, 4lf, 67, 117,273,274 Apple MacIntosh II, 67 Apple MacIntosh Plus, 67 Apple MacIntosh SE, 67 DEC LSI-11 , 68 DEC microVAX, 68 DEC VAX, 68 DEC PDP-II, 67 DEC PDP-11/03, 68 DEC PDP-ll!23, 68 DEC PDP-1l!45, 68 DEC PDP-ll!73, 68 IBM AT, 40f, 64f, 65 IBM PC, 65 IBM PS/2, 66, 76 IBM XT, 65

lap-top, 65 mainframe, 13g Mark 11,74 microcomputer, 13g microprocessor, 13g, 64f minicomputer, 13g mother board, 14g, 63 use in neuroanatomy, review of, 70 OEM, 14g, 15g one-bus, 48 peripheral devices, 16g personal, 13g, 16g power supply for, 64f, 65

transformer, constant-voltage, 341, 345 processing speed of, 339, 365f, 366 processor, 336

array, 2g purchasing of, 68

testing program on own data, 85 think "software first," 85 vendor, 86 dilemma of, 86

real time, 18g standard of comparisons, 375 turnkey, 21g, 85, 366 two-bus, 48 use with telephone, 79

Computer science research with biological results, 386 Computer systems for neuroanatomy, commercial,

387 Computer-user interface, 265

command-line interface, 271, 272 programmer's viewpoint of, 273

continuity, preservation of concentrational, 276 tactile, 145, 276, 277 visual, 145,270, 276

dialogue box, 275, 275f directly viewed input, 145, 146 direct manipulation, 273, 274

advantages and disadvantages, 274, 275 documentation, see user manuals

Computer-user interface (cont. ) entering textual data, 275 feedback, need for quick, 268 graphical interfaces, 274, 274f, 275 help menus on-screen, 282

advantages and disadvantages of, 282 human factors engineering, 266 icons, I1g, 274, 274f

selection of, 275 interactions with a program, 268

orthogonality of, 15g interactive devices, 61, 266

to control tracing, 276 for selection, 276 switching modes, 276

INDEX

mental model of program's operation, 267 menus, 13g, 268

pop-up, 16g, 269, 270, 272f, 275 pull-down, 17g, 269, 270, 27lf, 275

for novice user, 84 obvious next step, 268 parameters

changing and maintaining, 276 setting of, 275, 276

presentation of output, 281 prompting of user

for data, 272 for parameter ranges, 280

responses of computer program, 266 scripting, 13g, 199, 271 scroll, 199 submenus, 199, 270, 270f tactile continuity, 145

preservation of, 276, 277 time-based point entry, 277 toolboxes, 273 typing, elimination of, 275 undo command, 274 use of wildcards, 10 1 user, 21g user friendly, 21g, 266, 267f user manuals, 282

cost of, 283 for reference details, 283 for strategy, 283 tutorials, 283

visual continuity, 145 preservation of, 270, 276

visual presentation of commands and data, 273 windows, 270

for display, 169, 169f controlling size and location with mouse, 139

Computer vision, cabilities and failures, 373 Concentration of neurotransmitters, 370 Concentrational continuity, preservation of, 276 Concentric, 6g Concentric spheres, 208, 212f Configuring systems for neuron tracing, 107 Confocal microscope, 381, 382f; see also

Microscope, confocal applied to automatic neuron tracing, 382, 383

INDEX

Confocal microscope (cant. )

characteristics of, 382 combining reflected- and transmitted-light images,

385, 385f components of, 382f confocal scanning principle, 383, 384f details of operation, 386 light path of, 382, 383, 383f results of image capturing, 384f, 385, 386 sharply-focused image, 385 spatial resolution, 382 time to capture image, 382 use of reflected light, 383 use of transmitted light, 383

Connectivity pattern of a tree, 216 Cononical variate analysis, 263 Constant-voltage transformer, 341, 345 Constraints in microscopy, 25, 26f, 27, 35 Continuation point, 95, 97, 99 Continuity, preservation of

concentrational, 276 tactile, 145, 276, 277 visual, 145, 270, 276

Continuous capture mode, 135 Contour maps, 318 Contrast, 6g

enhancement with look-up tables, 346 stretching, 286f, 290f

Control of devices computer system, 265 cursor diameter, 93, 93f focus with mouse, 135 microscope stage, 277

comparison of devices, 278 with joystick, 92

video cursor with mouse, 133 Controls, in immunohistochemistry, 363 Conversion of pixel-based image into vector-based,

373 Converter

analog-to-digital: see AID converter digital-to-analog: see DAC

Convolution of images, 6g, 308f choosing a kernel, 308f, 309f, 310 techniques for, 308f

Coordinate systems for graphics displays, 168, 168f for tracing, 94, 94f

Copy stand, 130 Core memory, 6g Correction coefficients, 339 Correction for size of brain in analysis of neurons,

262 Correction image, 339, 340 Corticotectal pathway, 370, 371 Corticotropin-releasing factor, 371 Cost of passive stage, 105 Cost of software, 81 Cost of software and hardware, 71, 82 Cost of statistical sampling, 260 Cost of video systems, 146

Counting measurements of, 194 of cells, 143, 143f

automatically, 144 clumps of cells, 143f of silver grains, automatically, 143 types of points, 195

Crash, 6g, 281 Critical flicker frequency, 5g, 6g Cross-hairs reticule, 118

used as a cursor, 105 Cross-sectional area, 195, 196f, 344

of a dendritic field, 196 Cumulative misalignment errors, 119 Current stage coordinate, 94 Cursor, 6g, 17g

control keys on keyboard, 269 diameter of, 95f

variable, 93, 103 use of, 97f

fixed position, 93 use in editing, 157f hand, 6g in microscope, 95f, 106f optically mixed with microscope image, 87 positioning on a video screen, 278 repositioning to next frame, 134 screen, 269 use of cross-hairs reticule, 105 use in serial section reconstruction, 113

Customer telephone support, 83 Custom programming, 82 Cut tissue edge, use in section alignment, 120 Cyanogen bromide, 364 Cylinder, 6g

DAB,360 concentration, 362, 363 reaction time, 362

DAC, 6g, 51 DI A converter: see DAC dB,7g DEC, 67, 68, 75; see also Digital Equipment

Corporation DMA, 7g, 8g DOS, 7g, 8g, 74, 272 Dage-MTI, Inc., 397, 397f, 398f Dapple Systems, 398, 399f Darkfield microscope illumination, 143 Darkness, 3g Data

453

compatibilities among tracing and video systems, 124

compression techniques, 122, 122f, 123f multiuser access to, 75 storage, 43, 278; see also Storage of data

in binary files, 162 format, serial section reconstruction, 121,

122 how to store on disk, 162 when to store on disk, 162

454

Data base, 6g fonnat, 103, 104f management, 6g, 79 manipulations of, 157 mathematical scaling of, 157 mathematical testing of, 157 storage, 103

in memory, 103 on disk, 103

pixel-based fonnat, 166 polygon-based fonnat, 166 reducing points in the data base, 160 vector-based fonnat, 166 visual inspection of, 158

speed of, 159 voxel-based fonnat, 188, 380, 386

Data bits, 6g, 62 Data tablet, 6g, 57, 57f, 58f

acoustic, 57, 58f calibration of, 114, 277

real units of, 116 cursor viewed in microscope, 116f errors in measuring, 126 measuring systems, 126

for trees, 126 puck, 6g, 17g, 57, 57f

use in tracing, 276 use in control of microscope stage, 277 using magnetostrictive technology, 57 stylus, 199 use in section alignment, 119, 120f use in serial section reconstruction, 113 use in tracing, 105, 114f, 115f, 116, 117, !l8f,

126, 276 time-based point entry, 277

use in video digitizing, 130 Daughter angle, 6g Daughter fiber, 7g Debug, 7g, 74 Decibel, 7g Decimal,7g Default

file specifications, 279 values, 275, 276

Defense, Department of, 81 Defining a program, 84 Deflection, 7g Degree,7g

of a tree, 228, 232, 237 of a tree segment, 230 of subtree pairs, 221

Deleting erroneous points using a video system, 135 Delimiting an object in an image, 314 Dendrites, see also Neurons; Trees

area of influence, 244 bending factor of, 195, 195f; see also Tortuosity cartesian grid analysis of orientation, 254, 255,

256f center-of-mass of, 250, 25lf, 253

vector to, 25lf

Dendrites (cont. ) density of, 254, 255

statistical testing of, 255 student t-test, use of, 255

diameter of, 243 endings of, 97, 99 extent of, 34f field of, 7g, 197,244

centroid of, 253, 254f cross-sectional area of, 196 index of flatness, 254f length of, 244 shape factor of, 344, 355

growth vs botanical trees, 214 lengths, 195, 243

vs branch order, 204f distribution of, 202 to tenninals, 244 vs thickness, 202, 204f total, 243

major axis of, 253, 254f

INDEX

multivariate comparisons of sets of variables, 262 plots of

stick figures, 189f with thickness, 190, 190f, 19If

presynaptic, 358 region of influence, 197, 202, 203f

surface area of, 197 spatial orientation, 250

using Chi-square to test, 221 spines, 36, 99

analysis of, 200 base of, 99 density of, 199 distribtion of, 20 If, 203f

vs thickness, 203f types of, 200, 200f

thickness, recording of, 97 tracking of: see Neuron tracing

Dendrogram, 36f, 209f; see also Schematic diagram of a neuron

Densitometry, 336 hardware for, 292 review of, 372 software for, 366 transfer function, 343, 344f

Density,7g average, 3g fiber, imaging measurement of, 368

Department of Defense, 81 Depth cues, 167

hidden-line and -surface removal, 173, 173f, 174f intensity variation, 173

value of, 173 smooth rotation, 178 stereo pairs, 175, 176, 176f

Depth of field, 149 Depth of focus, 7g

control of in image digitization, 292 increasing by image processing, 327, 328f

INDEX

Design of statistiCal tests of neuronal populations, 258

Destructive test procedure, 28 Devices

drivers for, 282 interactive, 57, 58; see also Interactive devices;

Computer-user interface mass-storage, 337 names of, 279 peripheral, 16g

Diagonal gradient extraction filters, 320f Dialogue box, 275, 275f Diameter

of a dendrite, 243 fiber, imaging measurement of, 368 of root segment, 244

Diaminobenzidine, 345, 347f, 360, 362; see also DAB

Differential interference contrast microscopy, 350 Digit, binary: see Bit Digital, 7g, 43 Digital Equipment Corporation, 67, 68, 75 Digital subtraction autoradiography, 330 Digital-to-analog converter: see DAC Digitized images

compression of data, 295 storage of, 295, 380f

on a Bernoulli box, 295 on compact disks, 296 on floppy disk, 295 on hard disk, 295 on magnetic tape, 295 on VCR, 296 on WORM, 296

Digitizer, 7 g Digitizing a tissue slab, 380, 380f

advantages of, 381 storage of data, 380, 381 time required, 386 using confocal microscope, 386

Dilation, 7g, 311, 31H, 336, 351, 356, 366 of gray-level images, 312

Dilution of primary antibody, 362 Diodes, linear arrays of, 293

use in scanning an image, 293 Direction of dendritic growth, 199, 210, 212f Directly-viewed input, 145, 146 Direct manipulation user interfaces, 273, 274

advantages and disadvantages, 274, 275 Direct memory access, 7g, 8g; see also DMA Directory of files, 7g, 75; see also Catalog of files

root, 18g Disk, 7g, 41, 46

access time, 45 cylinder, 6g diskette, 8g

flexible, 9g, 42 double-sided, 8g drives, 7g, 42 files. 278

Disk (cont. ) format, 9g, 75 laser video, 296 operating systems, 7g, 74; see also DOS optical, 15g RAM,17g sector, 199 single-sided, 199 track, 20g, 46 Winchester, 109, 22g, 46 WORM,296

Displays, see also Computer graphics algebraic clipping, 169 algebraic scaling, 172 aliasing problem in, 178, 179 of anatomical structures, options for, 189 artifical distortions, 172 center coordinate of, 172 depth cues, 167 dynamic raster hardware, 189 enriched, 36, 174f

artifically, 125, 166, 173 facets, 167, 185

borders of, problem with, 186 filling of, 185 illumination of, 185, 186 smoothing of boundaries, 186f, 187 surface-filled, 185

flicker, 178 limiting data to avoid, 178 spatial filtering to avoid, 178

hidden line removal, 173, 173f, 174f, 185f algorithms, survey of, 191

advantages and disadvantages, 175 check everything method, 174, 175 cost of, 174 mask method, 174, 175, 175f in neuroanatomy, 191 on polygon-based data, 173 in serial section reconstruction, 187 sorting by Z, 174, 175 sUITounder test, 174, 175, 187

hidden surface removal, 173 algorithms for, survey of, 191 cost of, 187 in neuroanatomy, 191 on pixel-based data, 173 pixel by pixel, 187

highlighting portions, 166

455

by varying brightness, 179, 180, 180f, 18H illusion of three dimensions on a two-dimensional

screen, 167, 168 joystick to control, 167, 168 kinesthesia, use of, 167 line generation, 176

hardware for, 176 in raster displays, 177 in vector displays, 177

line rejection, 170, 170f in anatomical displays, 170

456

Displays (cont. ) magnification, 166, 172

methods of changing, 172 matrix multiplication

hardware for, 168 motion, provided by still frames in sequence, 168 palette, 15g

of colors, 288 pipeline, 16g polygon, 122

planar, 167 from any position, 166 processor, raster, 181 projection

disadvantages of, 241, 242f orthographic, 170, 171f, 172

flaws of, 172 of trees, 248 value of, 172

perspective, 171f distortion in, 171f division, 171

cost of, 171 hardware for, 171

one-point, 170 pseudocolor, 17g, 288, 345, 346, 347f, 367

exaggerating a small difference, 330 mapping, 303, 303f, 304f

raster, 17g, 52, 181 aliasing problem, 182, 183f of anatomical structures, techniques, 192 cost of, 183f, 188, 189 dynamic, cost of, 189 enriched, 187, 187f, 188 hidden-surface removal, 184f image generation, 184 realism of, 181, 182f, 184, 184f, 186f, 187,

187f, 188f refresh hardware, 181 resolution, 183 serial section reconstruction, 183f, 184 spatial resolution, 188 staircase effect, 55, 160, 160f storage on disk, 188 storage requirements, 177 surface-filled, 184, 184f, 185, 186, 186f systems, 52, 54, 165, 167 tesseling, 184 tiling, 184

effect of, 185f use during tracing, 103 triangulating, 184

refreshed, l8g, 177 rendering of, 165, 167 Road to PI. Reyes, 182f scaled to fill screen, 172 in serial section reconstruction, 173f, 174f shaded, 165 smooth rotation, 158, 167

cost of, 168 coupled with kinesthesia, 167 of vector displays, 178

Displays (cont.) spatial resolution, 178, 179, 179f, 180f stereo pair, 38, 175, 176, 176f

aids for viewing, 176 angle between views, 176, 176f

INDEX

building of by image processing, 329, 329f of neurons, 242f stereopsis, 167 from video systems, 147

of structures in environment, 166, 180f internal and external, 166

surface-filled, 184, 184f, 185, 186, 186f tesseling, 184 three-dimensional, 165

goals, 165 of neurons, 242f superb quality, 166f use of supercomputer, 166f with varifocal mirror, 192

tiling, 185f transparent surfaces in, 166, 187, 187f triangulating, 184 using varifocal mirror, 192 vector, 52, 55, 165, 167, 177, 178f

advantages during tracing, 103 color, 180, 181

beam penetration, 181 cost of, 180 ROB, 180

data representation, 129, 130, 373 conversion from pixel-based, 373

monochrome, 179 of serial section data, 123 storage requirements, 177 of structures, 122, 134

viewing small details, 179, 180f, 18H viewing volume, 170 voxel-based image representation, 188, 380, 386 windows, 169, 169f wire-frame, 55f, 56f, 165, 167, 173f, 178, 178f

without texture, 178 vector versus raster performance, 189

zooming, 22g, 166, 172,355 dynamic, with perspective divider, 172 static, 172

Distance-based point entry during tracing, 277 Distinguishing among structures during tracing, 89 Distortion in perspective projection, 17lf Distribution

of branch segment lengths, 202, 205f of dendritic length, 203f of Rail's ratio, 207, 208, 21lf of tapering, 206, 207f, 208f of tree types, 219

Distribution axis, in graph summaries, 200 Dithering, 190, 191 Dividing an image into regions, 314 Documentation of a program, 267

user manuals, 282 cost of, 283 for reference details, 283

INDEX

Documentation of a program (cont.) user manuals (cont. )

for strategy, 283 tutorials, 283

Dot continuation point, 102, 103f Dot end, 102, 103f Dot matrix printer, 165

for printing images, 130 Dot point, 122 Dot start, 102, 103f Double-sided disk, 8g Dragging, 125

and attach, 157 use in editing, 157 use of interactive device, 157

Drawing with camera lucida, 29f, 30f, 31

three-dimensional, 38 tissue sections, 113 tube, 31; see also Camera lucida

use during tracing, 116f Draw point, 122 Drivers, device, 282 Drum scanner, 334 Dyes, voltage-sensitive, review of use, 331 Dynamic range, 338 Dynamic raster display hardware, 189

EBCDIC,8g EGA, 8g, 47, 288 EIA,8g EPROM,8g Eayrs concentric-circles analysis, 247 Economics of computing, 82

company size, 85 cost of software, 81 cost of software and hardware, 71, 82 customer telephone support, 83 investment in software, 82 laboratory as a cottage industry, 78 profit, short term, 86

Edge detection, 8g filters for, 321 techniques for, 147

Edge enhancement, 8g, 346 filters, 318, 321 operator, 348f, 349f, 356

results of, 361f Edge-finding operators, 351 Edge-following algorithms, 315, 318f Editing, 8g

binary editing of an image, 356, 358 changing individual parameters, 155 deleting points, 155

using a video system, 135 dragging and attaching, 125, 157 erroneous point, finding, 158 global, 155, 156 highlighting the identified portion, 156, 157f identification of structure

by name, 156 by number, 156

Editing (cont.) identification of structure (cont. )

of point, 153f, 156 by pointing, 156 a range of points, 156 a structure, 125

of an image, 314, 348f, 349f interactive, I1g

binary, 355 results of, 352f, 353f

single point, 155 of traced data, 155 undo command, 274 use of cursor, 157f

Effort required to program, 265 Eikonix, Inc., 399, 400f, 40 If Electron beam, 52 Electron gun, 8g Electronic mail, 79 Electronic yellow pages, 79

457

Electron microscope, see also Microscope, electron calibration of, 337 photos from, 114f

Elementary summaries of a structure, 137f, 193, 194, 194f, 195

Elongation of dendritic field, measure of, 254 Ending,8g End swelling, 99 End user, 8g Enhanced graphics adapter, 8g, 288; see also EGA Enriched raster displays, 187 Enriched view of reconstruction, 109 Enriched view of structure, 36 Entering point types using a video system, 136 Entering textual data, 275 Entering thickness using a video system, 135 Epileptic seizures, 370 Equations, algebraic, 77 Equipment, bum-in of, 4g, 294 Erasable programmable read-only memory: see

EPROM Erosion, 8g, 311, 31 If, 336, 351, 356, 366

of gray-level images, 312 Errors, see also Computer-user interface; Editing

correction of, 149 in traced data, 155, 158

handling of, 280 beeping, 280 checking valid entries, 280 erasing a file, 280 mathematical errors, 280 principles, 281 reading and writing files, 280 warnings, 281

keyboard entry, 280 Errors, cumulative misalignment, 119 Errors in measuring on tablet, 126 European television standards, 288 Eutectic Electronics, Inc., 400, 402f Even parity, 62 Executable file, 73, 73f Execution of programs, 72

458

Expansion slot, 8g Experience of program user, 84, 271, 273 Extended binary-coded decimal code for information

interchange: see EBCDIC

FFf, 325; see also Fast Fourier transform Facets, 167, 185

borders of, problem with, 186 filling of, 185 illumination of, 185, 186

Fan-in projection, 249 Fast Fourier transform, 325 Feature enhancement

effects of, 322f, 323f, 324f, 325f filters, 318, 319f, 320

limitations of, 321 Feature extraction, 145, 350

filters, 318, 319f limitations of, 321

Feedback, 268 immediate, 274 from a program, 268 during tracing, 89 visual, 143f, 144, 145, 156,277,278

Felt-tip pen plotter, 165 speed of, 189 use in anatomy, 189

Fiber density, imaging measurement of, 368 Fiber diameter, imaging measurement of, 368 Fiber swelling, 99 Fidelity of image, 146 Fiducial marks, 120, 155 Field,9g

area of, 356 irregular boundary, 356

axonal,3g dendritic, 7g

centroid of, 253, 254f cross-sectional area, 196 elongation, measure of, 254 index of flatness, 254f mean diameter, 197

calculation of, 196 measurements of, 356

depth of, 149 interlace, 9g

one-to-one, 14g primary field, 17g, 53f

perimeter, 196f, 197, 344 calculation of, 196

primary, 9g, l7g receptive, of a neuron, 197 shape factor of, 344, 355

Files, 9g, 72 access to, types of, 75 ASCII, 2g, 78, 79

advantages and disadvantages, 163 batch,73 binary, advantages and disadvantages, 162 catalog of, 75, directory of, 7g, 75

Files (cont. ) executable, 73, 73f extensions, 9g, 278, 279 finding, 275, 275f, 276 locating, 275, 275f, 276 names, parts of, 278, 279 object, 72 opening, 15g for parameters, personalized, 276 patching of, 74 random access, 45, 123, 123f, 124 run, 73 save, 73 scripting, 73 security, 75 sequential, 123f serial, 123, 123f, 124 source, 72, 80f

translation of, 72, 73f, 76 specifications

default, 279 power of, 279

Filters blur-removing, 3g, 298f, 322f, 323f, 325f color, 146, 345 contrast-increasing, 345 data base, 159 edge-detection, 321 edge-enhancing, 318, 321 feature-enhancing, 318, 319f, 320 feature-extracting, 318, 319f Gaussian, 350 gradient-extracting, 320f

diagonal, 320f horizontal, 320f vertical, 320f

image-transforming, 319f, 336, 346 infrared, 146 justification for, 159 kernels, selection of, 320 LaPlacian, 350 line, 320, 321 low-pass, 160, 160f neutral-density, 342f, 343 notch,326 point-removing, 125 point-smoothing, 125, 159 radius-of-curvature, 161, 162f

justification for, 161, 162f for schematic effect, 161, 16lf, 162f smoothing: see Filters, low-pass spatial, 101, 117, 134, 160, 16lf, 277

domain, 288, 321, 325 for dots, 117 logical operations with, 310

INDEX

mean, of images, 308f, 309, 309f, 310, 310f median, of images, 308f, 309, 309f, 310,

310f Finding a data file, 275, 275f, 276 Finding programming personnel, 86 Firmware, 9g, 46, 69

INDEX

First-order tree partitions, 219, 219f, 22Ot, 221, 222f, 223, 223f, 233, 238

Fixed position cursor, 93 Flat-bed scanner, 9g, 334 Flexibility of program, 84

vs learning time, 273 Flexible diskette, 9g, 42; see also Floppy disk Flicker, 9g, 177

critical frequency, 5g, 6g prevented in raster displays, 181 time constraint, 177

Flight simulation, graphics displays in, 171 Floating point numbers, 43 Floppy disk, 9g, 42, 46, 64f Fluorescence

dyes, 336 intensity, 371 techniques in microscopy, 333

Focus automatic, 144, 144f

history of, 147 axis

backlash, 159 problems, 149, 150f readings, inaccuracy of, 149, 159, 163

unwanted refraction, 150, 150f, 163 changing during tracing, 99f controlling by computer, 145 depth of, 7g

control of in image digitization, 292 increasing by image processing, 327, 328f

plane of, 144 Format,9g

disk, 75 Form factor, 196f, 197,344,355

calculation of, 196 Forms of computer data, 43 FORTRAN, 73, 77, 79, 80f Fortran-77, 79 Fourier

analysis of images, 321, 325 frequency filtering, 326 space, 325 transform, 9g

imaging hardware needs of, 288 Frame buffers, 9g, 54, 129, 181,288,336,367

multiple, 291, 292 Frame grabber, 109, 130 Freehand drawing from microscope, 23, 24 Frequency, critical flicker, 5 g Frequency compensation of images, 326 Frequency domain, 325 Frequency spectrum, 325 Frequency variables, 325 Full automation of mundane tasks using video, 145 Full neuron overlay, 98, 100f

GABA, 347f, 348f, 349f, 357f, 358, 359f, 362, 365f, 369, 371

GM-l ganglioside, 370 GPIB, 109; see also IEEE-488 bus

Gain and offset, in video, 297 Gamma, tOg, 293

459

Gamma-aminobutyric acid, 347f, 348f, 349f, 357f, 358, 359f, 365f

Gamma-L-glutamyl-L-glutamate antibody, 372 Gelatin, 364 Gel electrophoresis, software for, 366 General Imaging Corporation, 403, 403f, 405f General purpose business software, 79 General purpose interface bus: see IEEE-488 bus Generating a mask using a mouse, 141 Geometry of cells, measurements of, 368 Ghost, 109 Gigabyte, 45 Glutamate, 356, 370, 371 Glutaraldehyde, 364 Gonadotropic-releasing hormone, 362, 370, 37t Grab, 109 Gradient-enhancing filters, 346 Gradient-extraction filters, 320f Gradient operators, 350 Graphical interfaces, 274, 274f, 275 Graphics, see also Computer graphics; Displays

Bit-mapped, 47 display cards for, 42, 46

CGA, 2g, 5g, 47, 288 EGA, 8g, 47, 288 MDA, 13g, 14g, 47 MGA, tOg, 13g, 47 VGA, 21g, 47, 66, 288

display systems, 52 editor, use during tracing, 118f film recorder, 335f

Graphs, 193, 200 automatic scaling of, 281 hard copies of, 28t interactive editing of, 281 paper copies of, 281 user control of format, 281

Gray levels, 109, 336, 338, 339, 340, 341, 343, 346,350

enhancing of, 345 histogram of, 109, 339, 357f images, applying erosion and dilation, 312 information, 130 operators, 346, 350, 366

software for, 366, 367 profile, 144

of best focused image, 145 of a line, l40f

range, 130 used in cell counting, 144

resolution, 34t transformation, 367

Gray scale, 338 analog adjustments, 297 resolution, 365f

of scanner, 334 stretching, 302 transformations, 288, 290f

Grouping neurons for statistical comparisons, 257

460

Growth botanical tree vs dendritic tree, 214 model of neuron trees, reference to, 214

HDTV, 109, 288 HPm, 11g, 63; see also IEEE-488 bus HPLC,371 Half-spaces of volumes, 250 Halovision image editor, 274 Hand cursor, 6g, 109, 17g

use in section alignment, 119, 12lf use in tracing, 276

Handler, 109 Hard copy, 17g, 165, 189 Hard disk, 109, 41, 46, 64f, 337 Hardware, 109, 39, 71

compatibility, 5g, 69 computations to overcome hardware constraints,

163 cost of, vs software, 71, 82 for image processing, 337, 368 mass production of, 82 matrix multiplier, 168

Harvard University, 74 Heading, compass, 198f Help menus on-screen, 282

advantages and disadvantages of, 282 Hercules Corporation, 47

monochrome display adapter, 109; see also MDA

monochrome standard, 288 Hewlett-Packard instrument bus, 63; see also

IEEE-488 bus Hexadecimal, 109 Hexant region of a cube, 251, 252f Hidden-line removal, 173

algorithms, survey of, 191 advantages and disadvantages, 175

check everything method, 174, 175 cost of, 174 mask method, 174, 175, 175f in neuroanatomy, 191 on polygon-based data, 173 in serial section reconstruction, 187 sorting by Z, 174, 175 surrounder test, 174, 175, 187

Hidden-surface removal, 173 algorithms for, survey of, 191 cost of, 187 in neuroanatomy, 191 on pixel-based data, 173 pixel-by-pixel, 187 on voxel-based data, 188, 380, 386

Hierarchy of menus, 270 High-density television, 109, 288; see also HDTV High-fidelity image, 90 High-level language, 109, 77, 366

proprietary, 81 Highlighting the identified portion for editing, 156,

157f Highlighting by varying brightness, 179, 180, 180f,

18lf

Hippocampus, 371 Hiring a programmer, 84 Histochemistry, 355

procedures and controls, 360 Histogram, 356

of cell sizes, 359f equalization, 302 of gray levels, 302, 339

Horizontal gradient extraction filters, 320f Horizontal scan lines, 109 Horizontal sync pulses, 109, 53 Horsfield ordering, 230f, 236 Hot spot, 11g Hue,l1g Human factors engineering, 266 Human pattern recognition, 89 Human vision

abilities and failures, 373 as many parallel computers, 375

Hydrogen peroxide, 362 concentration of, 363

Hypothalamus, 370, 371

IBM AT, 40f, 64f, 65 image processing software for, 368

IBM PC, 65 IBM XT, 65 IC, Ilg, 63; see also Integrated circuit IEEE-488

bus, Ilg port, 63

INDEX

IOD, 3g, 11g, 12g, 338, 343, 350, 356; see also Integrated optical density

Icons, Ilg, 274, 274f selection of, 275 use during tracing, 119

with a video system, 135, 138f Identification of structure for editing

by name, 156 by number, 156 of point, 153f, 156 by pointing, 156 a range of points, 156 a structure, 125

Illusion of three dimensions on a two-dimensional screen, 167, 168

Image, llg; see also Image processing acquisition, 346

devices for, 334 speed of, 337, 338

analysis, Ilg, 344 systems for quantitative immunocytochemistry,

335f, 336, 337 systems for specific applications, 367

artifacts of known characteristics, corrections for, 313

averaging, Ilg choosing a kernel, 308f, 309f, 310 to reduce noise, 346 spatial, 308f techniques for, 308f using video, 145

INDEX

Image (cont.) background, 3g binary, 350, 355

off pixels, 122 on pixels, 122

blurred, corrections for, 313, 314 boundary of, 351 brightness during tracing, 103 of cells, 368 colors, primary, 287f, 302, 303, 303f compression of data in, 295 contour-map generation, 318 contrast, 6g

enhancement of, 345 with look -up tables, 346

sharpening, 350 stretching, 286f, 290f

conversion of pixel-based into vector-based, 373

convolution of, 6g, 308f correction, 339, 340 darkness, 3g delimiting an object, 314 digitization into pixels, 146 digitizing hardware, 129 dithering, 190, 191 dividing into regions, 314 edge enhancement, 350, 366 editing, 314

controlling a cursor for, 314 Halovision image editor, 274

elements of: see Pixel Pel, 16g

enhancement, 11g, 129, 138, 296 analog, 296, 297 categories of, 296 Fourier analysis, 297, 325, 326 frequency-domain techniques, 296, 297 spatial-domain techniques, 296, 297 types of, 285 use in cell counting, 143f, 144 value of, 286f

feature detection, 315 fidelity of, 146 field measure, 355, 368 filter

mean, linear, 350 spatial, 101, 117, 134, 160, 16lf, 277

domain, 288, 321, 325 for dots, 117 logical operations with, 310 mean, of images, 308f, 309, 309f, 310, 310f median, of images, 308f, 309, 309f, 310,

310f in fluorescence microscopy, 306f out-of-focus correction, 313, 314, 322f, 325f Fourier

analysis of images, 321, 325 frequency domain in, 325

frequency filtering, 326 space, 325 transform, 9g

Image (cont.) frame, 351, 354f

of measurement, 350 frequency compensation of, 326 frequency spectrum of, 325 frequency variables of, 325 geometric measurements, 343 gray-scale range, 345 hard copy of, 17g, 165, 189 high-fidelity, 90 histogram, I1g, 356

equalization of, 302 of gray levels, 302, 339

hot spot in, I1g keying between two, 292 masking of, 141, 142f, 308f measurements, 355

algorithms for, evaluation of, 343 biological utility of, 369 of neurons, 369 software for, 36lf, 366

memory, 338, 340, 366 movement in, sensing of, 61, 312 noise reduction, 366 object detection in, 346 objects extracted from

area, 355 breadth, 355 center of gravity, 355 descriptors, 355 height, 355 length, 355 orientation, 355 perimeter, 355 width, 355

object-selection algorithm, 358 operators

binary, 366 closing, 5g, 311, 31lf, 351, 356 dilation, 7g, 311, 311f, 336, 351, 356,

366 of gray-level images, 312

erosion, 8g, 311, 31lf, 336, 351, 356, 366 of gray-level images, 312

fast Fourier transform, 325 opening, 15g, 311, 31lf, 351; 366 thinning, 336, 355, 366, 369

results of, 352f, 353f optical density, 15g, 38, 334, 338, 344, 354f,

356, 357f, 370, 371

461

measurements of, 129, 136, 138, 346, 363, 368

software for, 367 pseudocolor, 17g, 288, 345, 346, 347f, 367

exaggerating a small difference, 330 mapping, 303, 303f, 304f

rescaling difficulties of, 326f using Fourier transforms, 326

rotation of images difficulties of, 326f using Fourier transfomls, 326

462

Image (cont.) run-length encoding of, 295 scanner of, 366 segmentation, 315, 348f, 349f, 350, 354f, 356,

360, 366, 368 by threshold, 315, 316f, 317f

sensor of, 292, 338 in serial section reconstruction, 113 shading correction, 346,366 sharpening, 346

from out-of focus, 322f, 325f storage of, 295, 380f

on a Bernoulli box, 295 on compact disks, 296 on floppy disk, 295 on hard disk, 295 on magnetic tape, 295 on VCR, 296

advantages and disadvantages, 296 spatial resolution, 296

on WORM, 296 three-dimensional, building of, 327, 328f thresholding, 20g, 310, 336, 350

local, 315 real-time, 367

transformations, 285, 319f transmittance, 21g, 338 uneven illumination, corrections for, 312 vector-based, 129, 130, 373

conversion from pixel-based, 373 of serial section data, 123 of structures, 122, 134

whole field, 351 Image analyzers, 287f, 334, 338, 339, 355, 356,

357f, 361f, 365f, 370 cell measurements by, 356, 358 continuous capture mode of, 135 drift, long-term, 343 dynamic range of, 338, 343 frame buffers, 9g, 54, 129, 181, 288, 336,

367 multiple, 291, 292

frame grabber, 109, 130 hardware for Fourier analysis, 288 for immunocytochemistry, 334, 343, 372

commercial,366 linearity of, 339, 343 magnification factor, 345 nonlinearities in, 339 photodetectors for, 334 photomultiplier tube, 16g, 292 pipelined, 16g, 367 resolution of, 366 sensitivity of, 336, 343 temporal variability, 339

long-term, 341, 342f short-term, 341

transfer function of, 339 true color, 295

Image Data Systems, Inc., 404, 406f, 407f Image dissector, llg Image intensifier, 16g

Image processing, 11g; see also Image background subtraction, 3g, 329 binary transformations in, 336 color, using a monochrome camera, 295 combining images, 327, 328f, 329, 329f

by subtraction, 329 contour map generation, 318 delimiting an object, 314 densitometry, 336

hardware for, 292 review of, 372 software for, 366 transfer function, 343, 344f

density, 7g average,3g

depth of focus, 7g control of in image digitization, 292

digital subtraction autoradiography, 330 binary, 355

results of, 352f, 353f edge detection, 8g

filters for, 321 techniques for, 147

edge enhancement, 8g, 346 filters for, 318, 321 operator, 348f, 349f, 356

results of, 361f edge-finding operators, 351 edge-following algorithms, 315, 318f editing, interactive, I1g feature enhancement

effects of, 322f, 323f, 324f, 325f filters, 318, 319f, 320

limitations of, 321 feature extraction, 145, 350

filters, 318, 3I9f limitations of, 321

filters edge-detection, 321 edge-enhancement, 318, 321 feature-enhancement, 318, 319f, 320 feature-extraction, 318, 319f gradient-extracting, 320f

diagonal, 320f horizontal, 320f vertical, 320f

infrared, 146 low-pass, 160, 160f notch,326 spatial, 160, 161f

mean, 308f, 309, 309f, 310, 310f median, 308f, 309, 309f, 310, 310f

Fourier analysis in, 321

INDEX

gray levels, 109, 336, 338, 339, 340, 341, 343, 346, 350

enhancing of, 345 erosion and dilation, 312 histogram of, 109, 339, 357f information, 130 operators, 346, 350, 366

software for, 366, 367 profile, 144

INDEX

Image processing (cont. ) gray levels (cont.)

profile (cont.)

of a line, 140f of best-focused image, 145

range, 130 used in cell counting, 144

reference, 339 resolution, 341 transformation, 367

gray scale, 338 analog adjustments, 297 resolution, 365f

of scanner, 334 stretching, 302 transformations, 288, 290f

hardware for, 287, 287f, 367 ALU,291

Motorola 68000, 291 amount of arithmetic processing, 291 boards, 287, 366 coprocessors, 291 cost of, 287, 291 enhancement capabilities, 291 frequency-domain filtering, 291 IBM-AT compatible, 291 how to purchase, 287 resolution of, 366 spatial filtering, 291 special purpose, performance of, 375 video overlay, 291 VME-bus compatible, 291

in immnnocytochemistry, 334, 339, 352f, 353f inverse-image function, 360 legitimacy of, 330 limitations of, 324f locating regions automatically, 315

limitations on, 315, 316f, 317f measurements

of color levels of a pixel, 139f of gray level

of a pixel, 139, 139f of pixels in an area, 139 of pixels on a line, 139, 140f

of a neuron, 348f, 349f Nyquist sampling frequency, 14g operators, 366

gradient, 350 outlining a region defined by a threshold, 315 pattern recognition in, 35, 87, 132, 158 region of interest, 18g, 138, 140, 14lf, 368 reverse Fourier transform, 326 review of, 331 shading corrections

algorithms for, 339, 340f, 341 errors in, 340

significance of, artifically increasing, 330 silver grain counting with, 143 skeletonization, 355, 358 software for, 296, 368, 372

cost of, 296 for microcomputers, 368

Image processing (cont.) software for (cont. )

third-party, 367 stacking images by, 327, 328f stereo-pair building with, 329, 329f subroutines, 344 system

dynamic range, 337 gray-level resolution, 337 gray-scale resolution, 338 spatial resolution, 337

textbooks for, 371 toolboxes, 296

Image processor: see Image analyzers Imaging Research, Inc., 406, 408f Immunocytochemistry, 334, 365f, 368, 371

analysis of data linear regression, 365f

controls for, 363 negative, 363

data analysis of, 333

463

fiber density, imaging measurement of, 368 fiber diameter, imaging measurement of, 368 GABA, 347f, 348f, 349f, 357f, 358, 359f, 362,

365f, 369, 371 gelatin, 364 glutamate, 356, 370, 371 glutaraldehyde, 364 GM-l ganglioside, 370 gonadotropic-releasing hormone, 362, 370, 371 HPLC,371 hydrogen peroxide, 362

concentration of, 363 imaging techniques for, 334 immunoreactivity, 350, 363

area, imaging measurement of, 369 profiles of, 370 prolactin, 370

incubation times, 362, 363 indirect peroxidase, 360 innervation density, 358 kinetic reactions, 360

linear enzyme, 369 monocular segment of, 359f

labeling intensity, 344 leutinizing hormone, 371 of LGN, 348f, 349f, 354f, 356, 358, 359f, 360,

36lf, 369, ligand

bound, 368 concentration measurements, software for, 367

light pen, use of, 345 linear response of system for, 343 micropipettes, use of, 363 neurotransmitters, 333, 365f

concentration of, 370 nonbiological standards, 334, 365f, 371 nonbiological substrates, 364 nonspecific labeling, 363 normal serum controls, 363 off-center cells, 359

receptive fields of, 370

464

Immunocytochemistry (cont. ) on-center cells, 359

receptive fields of, 370 optical density

of concentration standard, 370 of segmented fibers, 369

ovariectomy, 370, 371 PAP, 360 peptide, 370 peroxidase, 363 PGN, 358, 359f photometric

measurements, 339 uniformity, 339, 340

in space, 339 in time, 341

pituitary, 371 polyacrylamide films, 364 presynaptic dendrites, 358 primary antibody, 363 prolactin immunoreactivity, 370 quantitative immunocytochemistry, 334, 337,

344, 360, 365f, 367, 369, 370 quantitative receptor autoradiography, 367, 368 radioimmunoassay, 370 radioligand work, standards for, 367 reaction

agents, 362 product, 333

reagent dilution, 363 receptor density measurements, software for, 367 reserpine, 370 review of, 372 scintillation counts, 371 secondary antibody, 362 serotonin (5-HT), 352f, 353f, 369 skeletonization, 355, 358 standards, 364, 371

of optical density versus concentration, 364, 365f step-wedge, 364

stria terminalis, 370 substantia inominata, 370 substantia nigra, 370 superior colliculus, 347f, 352f, 353f, 369, 370 testosterone, 370, 371 thinning, 336, 355, 366, 369

results of, 352f, 353f transmitters, 369, 370

pathways of, 358 tyrosine hydroxylase, 369, 370

antibodies to, 363 visual cortex, 356, 357f

areas 17 and 18, 357f W-type cells, 360, 369 Y -like cells, 360

Incomplete trees analysis of, 217, 236, 237 types of, 237

Incubation times, 362, 363 Indec Systems, Inc., 407, 408f Index of flatuess of a dendritic field, 254f Indirect peroxidase, 360

Inflection point, 11 g Infrared filters, 146 Inherent problems in software, 83 Innervation density, 358

INDEX

Institute of Electrical and Electronic Engineers, Ilg, 62; see also IEEE

Integers, 43 Integrated circuit, 11g, 44, 63, 64f; see also IC

silicon wafer in, 63 Integrated optical density, 11g, 140, 14lf, 144,

144f, 338, 343, 344, 350, 356 Intel Corporation, 65, 66 Intensified silicon intensifier target, 306f; see also

ISIT Intensity depth cueing, 173

value of, 173 Interacting with a program, 268 Interactive binary editing, Ilg, 355

results of, 352f, 353f Interactive devices, 61, 266

to control tracing, 276 data tablet, 6g, 57, 57f, 58f joystick, 12g, 58, 59f light pen, 12g, 356, 357f, 358, 360, 36lf

advantages and disadvantages, 269 use of in immunocytochemistry, 345

puck, 6g, 17g, 57, 57f for selection, 276 stylus, 199 switching modes of, 276 trackball, 20g, 60, 60f

Interest area of, 2g

Interlaced raster, 53, 53f Interlace field, Ilg, 53f Intc::rmediate computations of reconstructed data, 149

ten-to-one rule of vectors, 150, 15lf Intermediate segment, Ilg Interpoint distance histogram, 213, 213f Interpreted languages, 77 Interpreter, 11 g, 77 Interrupt, 12g Inverse-image function, 360 Investment in software, 82 Irregular boundary, area of, 356"~,,i

I,: """ Jaggies, Ig, 12g; see also Aliasing, problem ef ' Jandel Scientific, Inc., 409, 410f Joyce-Loebl, 411, 41lf, 412f

Magiscan, 367 Joystick, 12g, 58, 59f

to control displays, 167, 168 to control stage and focus, 277, 278

positional mode of control, 93 three-dimensional, 59f, 60 use during tracing, 92, 93, 93f, 105

Kbytes, 12g, 45 Keruel, 308f, 350

amendment pixels, 351 for image convolution, 6g, 308f, 309f, 310 orthogonality of, 320

INDEX

Keyboard. 12g, 42; see also Keypad, use during tracing

cursor control with, 269 for microscope stage control, 106, 277 program control with, 275 use during tracing, 91

Keying between two images, 292 Keypad, use during tracing, 91f, 94, 95; see also

Keyboard Kilobytes, 12g, 45 Kinesthesia, sense of, 167 Kinetic reactions, 360 Kruskal-Wallis statistical test, 261

LED, 12g, 61 LGN, 348f, 349f, 354f, 356, 358, 359f, 360, 361f,

369; see also Lateral geniculate nucleus laminae of, 356, 358, 359, 369

LSI-11, 68; see also PDP-11 Labeling intensity, 344 Laboratory as a cottage industry, 78 Languages

command,5g miscellaneous, 80 programming, 79

ADA, Ig, 81 ALGOL, Ig, 81 assembly, 2g, 76, 77 BASIC, 3g, 80, 80f C, 4g, 76, 79, 80f COBOL, 5g, 81 FORTRAN, 9g, 73, 77, 79, 80£ FORTRAN-77,79 high-level, 109, 77, 366

proprietary, 81 interpreted, 77 low-level, 13g, 77 machine, 13g Pascal, 16g, 81 PL/I, 16g, 81

translators for assembler, 2g, 76, 77 compiler, 5g, 72, 77 interpreter, 11g, 77 linker, 73

Lap-top computers, 65 Laser printer, 12g, 49, 50, 51f, 165

binary device, 190, 191 dithering to achieve gray scale, 190, 191 plots on, 190

method of generation, 190 for raster hard copy, 190 speed of, 191

Laser-scamIing microscope: see Confocal microscope

Laser video disks, 296 Lateral geniculate nucleus, 348f, 349f, 354f, 356,

358, 359f, 360, 36lf, 369 Length of dendrites, 344; see also Neurons, analysis

of -based measurements, 195

Lens, C-mount, 4g

Leutinizing hormone, 371 Libraries of subroutines, 282 Ligand

bound,368

465

concentration measurements, software for, 367 Light-emitting diode, 12g, 61 Light microscope, 335f, 344, 345, 359; see also

Microscope, light Light pen, 12g, 356, 357f, 358, 360, 36lf

advantages and disadvantages, 269 use of in immunocytochemistry, 345

Limiting regions of data with a mask, 141, 142f; see also Mask

Line filters, 320, 321 Line generation, 176

hardware for, 176 in raster displays, 177 in vector displays, 177

Line printer port, 62; see also Port, parallel Linear access, of memory, 45 Linear diode arrays, 293

use in SCamIing an image, 293 Linear enzyme kinetics, 369 Linear potentiometers on stage, 104 Linear regression, 365f Linear response, 343 Line rejection, 170f

in anatomical displays, 170 Linked list storage, 123f, 124 Linker, 73, 73f Locating

a data file, 275, 275f, 276 regions on an image automatically, 315

limitations on, 315, 316f, 317f structures in the tissue, 102, 103f

using a video system, 135, 138f Locomotor activity, of rats, 370 Locus coeruleus, 369 Logical operations on images, 310, 311, 31lf

closing, 311, 311f dilation, 311, 311 f erosion, 311, 31lf opening, 311, 311f

Long-term drift, 343 Long-term temporal variability, 342f Look-up tables, 12g, 287f, 288, 338, 346 Lotus 1-2-3, 79, 279 Low-level programming, 77 Low-pass filters, 160, 160f

MCA, 66; see also MicrochamIel architecture MDA, 13g, 14g, 47; see also Monochrome display

adapter MGA, 109, 13g, 47; see also Hercules Corporation MIN, 360, 36lf; see also Medial interlaminar

nucleus MS, 359f; see also Microsoft Corporation;

Monocular segment MS-DOS, 66, 75; see also Microsoft Corporation Macintosh, 4lf, 67,117,273,274 Macintosh II, 67 Macintosh Plus, 67

466

Macintosh SE, 67 MacPaint, 67, 117 MacWrite, 67 Machine-executable code, 73, 76 Machine language instruction, 76 Macro, 13g Macro capability, 271; see also Scripting Magnetic tape, 45, 46 Magnetostrictive technology, 57 Magnification factor, 345 Mail, electronic, 79 Mainframe, 13g Major axis

of a dendrite, 253, 254f of a structure, 199, 199f

Managing journal references, 79 Manipulation of data base, 157 Mannen, H., 31, 32 Manuals, user, 282

cost of, 283 for reference details, 283 for strategy, 283 tutorials, 283

Mapping, see also Serial section reconstruction; Tracing

cursor optically mixed with microscope image, 87 of neuronal environment, 101 optical encoder system on stage, 70, 104, 105 with pantograph, 15g, 31, 32f, 33f, 125 stage movement during, 101 use of polygons, 10 I

Mark II computer, 74 Marketplace

laboratory as a cottage industry, 78 for neuroanatomic computer systems, 387 neuroscience, 82

Mask,308f applied to images, 141, 142f use of mouse to generate, 141

Mass production of hardware, 82 of software, 82

Mass-storage device, 337 Master program, 74; see also Operating system Math coprocessor, 13g, 44

8087, Ig, 65 80287,65 80387,66

Mathematical models, 36 of data, 102 of structures, 163

Mathematical scaling of the data base, 157 Mathematical summarization of neuron structure,

193 Mathematical testing of the data base, 157

of surface points, 158, 158f Matrix multiplier hardware, 168 Maximal path length of a tree, 231 Maximum tissue thickness, 27 Mbytes, 13g, 45 Mean centrifugal order, 228, 230, 232

Mean degree of a tree, 230, 232 Mean diameter, 197

calculation of, 196 Mean PSAD, 225, 226f, 228, 232, 233

of multifurcating trees, 234

INDEX

Mean optical density, 140; see also AOD; Average optical density

Mean spatial filtering of images, 308f, 309, 309f, 310, 310f

Measured cell parameters area, 366 breadth, 366 cross-sectional area, 36lf length, 36lf, 366 optical density, 366 perimeter, 36lf

Measurements of branch segments, 244 of cells, 356, 358 of color levels of a pixel, 139f of details, 146 of gray level

of a pixel, 139, 139f of pixels in an area, 139 of pixels on a line, 139, 140f

of incomplete trees, 244 of metabolic rate, 38 of soma size, 242 of trees, 27, 194f

review of, 263 volume-based, 196

Media Cybernetics, Inc., 412 Medial interlaminar nucleus, 360, 361f; see also

MIN Median spatial filtering of images, 308f, 309, 309f,

31O,31Of Megabytes, 13g, 45 Membrane surface area, 196, 197f, 243 Memory, 40

capacity of, 13g cell, 45 core, 6g direct memory access, 7g, 8g EPROM,8g linear access, 45 main, 13g nonvolatile, 14g PROM,17g RAM, 17g, 40, 45

disk, 17g random access, 17g ROM, 18g, 45, 74, 75, 80

programmable, 17g tractable, 36, 87 volatility of, 22g, 45, 161 word, 43

Mental model of a program's operation, 267 Menus, 13g, 268

advantages and disadvantages of, 271 bar, 269 dynamic, 269

INDEX

Menus (cont. ) forms of display, 269 hierarchy of, 270 in microscope, 95 perimeter, 133, 274f

in microscope, 105, 106f pop-up, 16g, 269, 270, 272f, 275 pull-down, 17g, 269, 270, 27lf, 275 rigidity of, 273 on-screen help, 282 selection from, 269, 269f selection of, 84 submenus, 199, 270, 270f use in tracing, 91

Merging multiple-section trees, 152, 153f, 236 computer-generated overlay for, 152, 153f criteria for, 154 necessity of, 154 success rate for, 154 after tracing, 152, 154, 156f during tracing, 152, 153f

Metabolic rate, 38 Metric analysis of neuronal populations, 241 Metric characteristics of neurons, 216 Microchannel architecture, 66; see also MCA Microcomputers, 13g

image processing software for, 368 selection of, 70

Micrometer, stage, 345 Micropipettes, 363 Microprocessor, 13g, 64f Microscience, Inc., 413, 413f, 414f Microscope

confocal, 381, 382f applied to automatic neuron tracing, 382, 383 characteristics of, 382 combining reflected- and transmitted-light

images, 385, 385f components of, 382f confocal scanning principle, 383, 384f depth of focus, 7 g details of operation, 386 image capturing, results of, 384f, 385, 386 light path of, 382, 383, 383f optical sectioning, 15g, 113, 327, 328f sharply focused image, 385 spatial resolution, 382 time to capture image, 382 use of reflected light, 383

disadvantages in neuron tracing, 385 use of transmitted light, 383 wavelength, 345

electron calibration of, 337 photos from, 114f

light, 344, 345, 359 camera lucida for, 28, 29, 29f, 3lf computer-generated overlay in, 98 constraints of, 25, 26f, 27, 35 cursor, presented in, 95f, 106f darkfield illumination, 143

Microscope (cont.) light (cont.)

differential interference contrast, 350 drawing from, freehand, 23, 24 feedback in, during tracing, 95f, 97 fluorescence techniques, 333, 336, 371

imaging for, 306f focus

axis backlash, 159 motors on, 61, 91 problems, 149, 150f readings, inaccuracy of, 149, 159, 163 unwanted refraction, 150, 150f, 163

depth of, 7g, 381

467

control of in image digitization, 292 increasing by image processing, 327, 328f

plane of, 144 coordinate presented, 97

magnification of, 27 motor controller for, 14g, 70 Nomarski optics, 350 numeric aperture, 14g optical sectioning, 15g, 113, 327, 328f parfocal lenses, 16g perspective, 27 photomultiplier tube, 16g, 292 plotter, 31, 32, 32f, 125 projecting, 113f, 115f scanning stage, 292 stage, 277, 345

comparison of contolling devices, 278 control by joystick, 92 controller, 14g, 70, 367 cost of passive, 105 current coordinate, 94 joystick to control, 277, 278 micrometer, 345 motors on, 61, 91, 277, 335f 346,367 movement during mapping, 101 optical encoder system on, 70, 104, 105 passive during tracing, 104

resolution of, 105 potentiometers on, 104 reticule, 345 scanning, l8g

cost of, 292 time to acquire an image, 292

shaft encoders on, 61 stepping, 199 trackball to control, 277

televised image from, 129, 130 tissue thickness, maximum, 27 unwanted refraction, 150, 150f, 163 use of computers to control focus, 145 view during mapping, 102f viewing medium, 25 wavelength, 345 working distance of, 107

Microsoft Corporation, 66, 75 Microtome accuracy, 150

468

MicroVAX,68 Middle artificial end, 99 Middle tree origin, 96, 98 Minicomputer, 13g Minimal path length of a tree, 231 Mixing computer graphics image with microscope

image, 107 Models

of neuron growth, 217 physical, 32, 33f, 34f, 35

wooden blocks, 34f, 35 of segmental growth, 199, 221, 222f, 224 of terminal growth, 20g

Modem, 13g, 51 null, 63

Modulator-demodulator, 13g, 51; see also Modem Module, 13g; see also Board; Card; Subroutine Monitor, 13g; see also Television, monitors

RGB/TTL, 17g Monochrome display adapter, 14g; see also MDA Monocular segment, 359f Mother board, 14g, 63 Mother fiber, 14g Motion, provided by still frames in sequence, 168 Motorola Corporation, 67 Motors

controller for, 14g on microscope focus axis, 91 on microscope stage, 91, 277, 335f 346, 367 stepping, 199, 61

on microscope focus, 61 on microscope stage, 61 use in video digitizing, 130

Mouse, 14g, 58, 58f, 59f advantages and disadvantages, 269 clicking, 269, 272f to control focus, 106 to control microscope stage, 277 to control programs, 269 to control tracing, 105, 106 to control video-based tracing, 278 to control video digitizing, 130 to generate mask, 141

Move point, 122 Moving cursor over stationary image, 134 Multifurcating trees, 225, 234 Multiplex, 14g Multisync monitor, 14g Multiuser access to data, 75 Multiuser operating system, 75 Multivariate comparisons of sets of dendritic

variables, 262 Multivariate principal-component analysis, 262, 263

NA, 14g; see also Numeric aperture NTSC television standard, 14g, 288 Names

of devices, 279 of trees, 101

National Library of Medicine, 79 National television systems committee, 14g

Natural end, 99 Natural logarithm, 338 Negative controls, 363 Neocortex, 370 Nested analysis of variance, 258, 261 Nested statistical test design, 258 Neuroanatomy

INDEX

commercially available computer systems for, 387 computer applications in, review of, 371 marketplace for computers, 82, 387 use of computer graphics in

history, 191 special probems, 191

Neuron reconstruction, 87; see also Neuron tracing Neurons, see also Trees _

analysis of, see also Topological analy§is of neurons

clustering of points, 213, 213f Poisson distribution of, 213

dendritic length, distribution of, 203f dendrogram, 36f, 209f destructive procedures, 28 distribution axis, in graph summaries, 200 Eayrs concentric-circles analysis, 247 elongation of dendritic field, measure of, 254 graphing summaries, 193,200 grouping for statistical comparisons, 257 growth into subregions

cube divided into regions, 250, 251, 252, 252f

half-spaces of volumes, 250 hexant region of a cube, 251, 252f octant region of a cube, 251, 252f quarter-hexant region of a cube, 252 sphere divided into sectors, 248, 249f, 250

inflection point, I1g length of dendrites, 195, 344 Kruskal-Wallis test, 261 major axis of a dendrite, 253, 254f mathematical summarization of structure, 193 mathematical testing of traced data, 157

of surface points, 158, 158f membrane surface area, 196, 197f, 243 multivariate comparisons of sets of variables,

262 multivariate principal-component analysis, 262,

263 nested analysis of variance, 258, 261 nested statistical test design, 258 numeric summaries of, 137f, 193, 194, 194f,

195 parametric and nonparametric testing, 260, 261 polar diagram, 210, 212f, 248 principal-axes analysis, 253, 254f

three-dimensional, 253, 254f projection, fan-in, 249 radial distance from the soma, 200 Rall's ratio

versus branch order, 21lf calculation of, 207, 210f distribution of, 207, 208, 21lf

INDEX

Neurons (cont. ) analysis (cont. )

schematic diagram of, 206, 209f segment lengths, distribution of, 202, 205f Sholl 35, 215, 216, 216f

schematic diagram, 36f, 206 concentric-spheres, 35f, 208, 212f, 247

including area correction, 208 tapering, 206, 207f, 208f, 243

of a branch segment, 206, 207f ratio, 206, 207f

versus branch order, 208f tissue shrinkage, effects on, 263 tortuosity, 195, 195f total dendritic length, 243 vector to centroid, 25lf vertex analysis, 228

ratio of, 228, 232 volume of, 196

cable properties of, 214 circumscribing by a polygon, 198f direction of growth, 199, 210, 212f displays of, three-dimensional, 165, 242f mathematical models of, 36 mathematical scaling of, 157 measurements of, see also Cells, measurements

of center of dendritic length, 198 center of gravity, 198 center of neuron, 198 center of surface area, 199

metric characteristics of, 216 physical models of, 32, 33f, 34f, 35

wooden blocks, 34f, 35 plots of

stick figures, 189f with thickness of dendrites, 190, 190f, 19lf

populations of, 28 design of tests for, 258 metric analysis of, 241 statistical analysis of, 241

receptive field of, 197 region of influence, 197,202, 203f

surface area of, 197 shapes of, 215 size relative to brain size, 262 smoothing of, 160, 160f spines, 36, 99

analysis of, 200 base of, 99 density of, 199 distribtion of, 20lf, 203f

vs thickness, 203f types of, 200, 200f

statistical summaries, review of, 213 stereo pairs of, 242f swellings, 36

versus branch order, 202f distribution of, 202f

trifurcations, 4g, 21g, 99, 234 frequency of occurrence, 234

Neurons (cont. ) varicosities, 99; see also Swellings visual inspection of, 158

speed of, 159 volume of, 196, 197f

Neuron tracing, see also Tracing automatic, 373; see also Automatic neuron

tracing automatic vs semi-automatic, 374f changing focus during, 99f computer-driven return to branchpoint, 98,

98f,

469

computer-generated overlay for merging, 152, 153f

configuring systems for, 107 coordinate systems for, 94, 94f current stage coordinate, 94 cursor for

cross-hairs reticule, 105 diameter of, 95f

variable, 93, 103 use of, 97f

fixed position, 93 optically mixed with microscope image, 87 presented in microscope, 95f

directly viewed input, 145, 146 display

of dots by name, 102 of select trees from data base, 10 1 use of wildcards, 101

filtering radius-of-curvature, 161, 162f

justification for, 161, 162f spatial, 160, 16lf

focus coordinate presented in microscope, 97 full neuron overlay, 98, 100f history of, 107 intermediate computations in, 149

ten-to-one rule of vectors, 150, 15lf manipulation of data base, 157 measurements of fine details, 146 microtome accuracy, 150 mixing computer graphics image with microscope

image, 91, 107 need for, 241 objectivity, computer versus human, 375 one pass over the data, 89 optical encoder system on stage, 70 pattern recognition in, 35, 87, 132, 158 perimeter menu for, 133, 135, 274f

in microscope, 105, 106f reducing points in the data base, 160 reflected light microscope, disadvantages in

neuron tracing, 385 return to branchpoint from ending, 134 slide origin, 199, 94 staining, 27

loss of, 99 tags, 95, 97,101,102, 102f, 194 thickness measurements, 97

by circular cursor, 95f

470

Neuron tracing (cont.) thickness measurements (cont.)

without circular cursor, 105 tissue shrinkage, 150

correction for, 149 effects on statistical analysis, 263

tissue wrinkling, 150, 151, 15lf correction for, 149, 151, 152f

types of points, 98 bottom artificial end, 98f, 99 bottom tree origin, 99 continuation point, 95, 97, 99 dot continuation point, 102, 103f dot end, 102, 103f dot start, 102, 103f ending, 8g end swelling, 99 fiber swelling, 99 middle artificial end, 99 middle tree origin, 96, 98 natural end, 99 outline continuation point, 10 I, 102f outline end, 10 I, 102f outline start, 101, 102f soma continuation point, 95f, 102 soma outline end, 96, 96f, 102 soma outline start, 95, 102 special, selected from perimeter menu, 134 spine base, 99 top artificial end, 99 top tree origin, 99

UNC system, 90 use of camera lucida, 91, 116f use of in morphology, 107 using joystick to control, 92, 93, 93f, 105 using video,

entering point types, 136 entering thickness, 135

vector displays, advantages of, 103 Neuroscience marketplace, 82 Neurotransmitters, 333, 365f

concentration of, 370 Neutral-density filter, 342f, 343 Newvicon, 293 Noise

algorithms for correction of, 341 in biological images, 144, 285, 375 long-term in image, 341 in the video signal, 305

Nomarski microscope optics, 350 Nonbiological standards, 334, 365f, 371 Nonbiological substrates, 364 Noninterlace, 14g Nonlinearities in image analyzers, 339 Nonlinear transformations, 338 Nonspecific labeling, 363 Normal serum controls, 363 Notch filtering of images, 326 Novice user, 84 Nu-bus.67

Null modem, 63 Numbers

binary, 3g, 43 decimal,7g digital, 7g, 43 floating point, 43 hexadecimal, 109 integers, 43 octal, 14g scientific notation, 44 two's complement, 43

Numeric aperture, 14g Numeric summaries, 193, 194, 194f, 195 Numeric tag values, 101, 102, 102f Nyquist frequency, 14g

00, see Optical density OEM, 14g, 15g; see also Original equipment

manufacturer OS/2, 76; see also Operating system/2 Object detection in images, 346 Object file, 72 Objectivity, computer versus human, 375 Objects extracted from an image

area, 355 breadth, 355 center of gravity, 355 descriptors, 355 height, 355 length, 355 orientation, 355 perimeter, 355 width, 355

Object-selection algorithm, 358

INDEX

Obvious next step in program interactions, 268 Octal, 14g Octant region of a cube, 251, 252f Odd parity, 16g, 62 Off-center cells, 359

receptive fields of, 370 Off pixels, 122 Olympus Corporation, 414, 415f On-center cells, 359

receptive fields of, 370 On pixels, 122 One-bus computer, 48 One pass over the data, 89 One-point perspective projection, 170 One-to-one interlace, 14g Opening, of files, 15g Opening operation on images, 15g, 311, 31lf, 351,

366 Open loop system, 14g Open polygon during mapping, 101 Operand, 15g Operations

arithmetic, 2g, 44 binary, 351

on images, 366; see also Image processing software for, 366, 367

INDEX

Opemtions (cont.) Boolean, 3g, 44 for combining images, 336; see also Image

processing logical, 12g

on images, 310, 3U, 3Uf, 351, 356; see also Image processing

Opemting system, 15g, 73, 74, 337 [K)S, 7g, 8g, 74, 272 MS-DOS, 66, 75 multiuser, 75 OS/2,76 RT-ll,75 single user, 75 time sharing, 48, 75

time slice in, 75 UNIX, 76, 79

Operating System/2, 76 Optical density, 15g, 38, 334, 338, 344, 354f, 356,

357f, 370, 371 of concentmtion standard, 370 measurements of, 129, 136, 138, 346, 363, 368

software for, 367 of segmented fibers, 369

Optical disk, 15g Optical encoder system, 70 Optical mixing

of computer display and image, 91 of cursor and microscope image, 87

Optical sectioning, 15g, II3, 327, 328f Optical shaft encoders, 105

on stage, 104 Options for display of anatomical structures, 189 Order, branch, 4g, 15g, 95f, 97, 201

centrifugal, 5g, 230f, 235, 236, 245f for apical dendrites, 246f sum of, 228, 230 of a tree, 228 of tree segments, 218f

centripetal, 5g, 230f, 235, 236 Horsfield, 230f, 236 Stmhler, 23Of, 236 of tree segments, 163, 230f, 235, 236 use in metric analysis, 244, 245

Orientation analysis of

comparison of methods, 255, 256, 257 by cubic regions, 250 practical difficulties, 256, 257 by spherical sectors, 247, 248, 250 statistical tests for, 250 using stereo pairs, 250, 25lf

of a neuron, 199 of a structure, 199f

Origin, 15g slide, 199

Original equipment manufacturer, 14g, 15g Orthogonality, 15g Orthographic projection, 170, 172

flaws of, 172

Orthogmphic projection (cont. ) . of trees, 248

value of, 172 Outline continuation point, 101, 102f Outline end, 101, 102f

471

Outlining a region defined by a threshold, 315 Outlining a soma using a video system, 135, 136f Outline start, 10 1, l02f Outlining a structure using a video system, 135,

137f Ovariectomy, 370, 371

PAL television standard, 15g, 288 PAP,360 PC, 13g, 16g; see also Personal computer PC boards, 63; see also Printed circuit boards PDP-II,67 PDP-ll!03, 68 PDP-ll!23, 68 PDP-ll!45,68 PDP-1l173, 68 PGN, 358, 359f PIO, 16g; see also Progmmmed input/output pLlI, 16g, 81 PROM, 17g; see also Programmable read-only

memory PS/2, 66, 76; see also Personal Systeml2 PSAD, 225, 226f, 228, 232; see also Proportional

sum of absolute deviations for multifurcating trees, 234 of the soma, 235

Palette, 15g of colors, 288

Pan,15g Pantogmph, 15g, 31, 32f, 125

computerized, 125 Parallel port, 15g, 42

printer, 62 Parameter, 15g

changing and maintaining, 276 files of, personalized, 276 of imaged cells

area, 358 optical density, 358 perimeter, 358

setting of, 275, 276 Parametric and nonparametric testing, 260, 261 Parent fiber, 15g Parfocal, 16g Parity, 16g, 62

bit, 62 even, 16g, 62 odd, 16g, 62

Particle counting, 143, 143f, 145; see also Cells, counting of; Counting

automatic, 143f history of, 147

software for, 366 Partitions of trees, 218f, 219f, 228

all-order, 223, 225, 226f, 238

472

Partitions of trees (cQnt. ) of incomplete trees, 237 probability distributions, 224f

PASCAL, 16g, 81 PASCAL, B., 81 Passive microscope stage during tracing, 104

resolution of, 105 Patching a file, 74 Pathway, corticotectal, 370, 371 Pattern recognition, 35, 87, 132, 158 Patterns of branching, 209f Pedestal voltage, 297 Pel, 16g; see also Picture element; Pixel Peptide, 370 Percentage error, 341 Performance of special purpose hardware, 375 Perigeniculate nucleus, 358, 359f; see also PON Perimeter, 196f, 197, 344

calculation of, 196 Perimeter menu, 133, 274f

in microscope, 105, 106f Peripherals, 16g Peroxidase, 363 Personal computer, 13g, 16g Personal System/2, 66 Perspective projection, 170

division required, 171 cost of, 171 hardware for, 171

value of, 170, 171 Phosphor, 16g, 53; see also CRT

persistence of , 16g, 177 causing ghost, 109

Photodetectors, 334 Photographs of tissue sections, tracing from, 113 Photometric

measurements, 339 uniformity, 339, 340

in space, 339 in time, 341

Photomultiplier tube, 16g, 292 Photo transistor , 61 Physical models, 32, 33f, 34f, 35 Physical sectioning, 113 Picture element, 16g, 129; see also Pel; Pixel Pin holes, use in section alignment, 120 Pipeline, 16g

image processor, 367 Pituitary, 371 Pixel, 16g, 47, 129,288,339

-based image, 117, 118f, 373 -based representation of structure, 122 -based to vector-based conversion of image, 132,

373 -by-pixel image combination, 327 chaining of, 122, 123f, 295 mea~urements of color levels, 139f measurements of gray levels, 139, 139f

in an area, 139 on a line, 139. 140f

Pixel (cont.) replication, 172 visibility in hidden-surface removal, 187

Planar polygons, 167 Plots, 165

with details shown, 190, 190f on a laser printer, 190

method of generation, 190 realism of, 189, 190f with soma filled, 190f, 19lf spatial resolution of, 190 of statistical summaries, 190 of stick figures, 189f of structures in their environment, 190,

191f

INDEX

with thickness of dendrites, 190, 190f, 191f of three-dimensional structures, 189 using color, 190

Plotters, 48 analog, 32 use in anatomy, 189 cost of, 190 felt tip pen, 9g, 48, 49f, 165

speed of, 189 multi-colored, 190 speed of calculations for, 191

Plotting light microscope, 125 Plumbicon, 293 Points

capturing automatically, 101 densities, 199 entry during tracing, 277 type distribution, 20 I, 20 If

Poisson distribution, 213 Polar diagram, 210, 212f, 248 Polling, 16g Polyacrylamide films, 364 Polygon, 122

area enclosed, calculating, 195, 196f circumscribing a neuron by, 198f closed, mapping, 101 closing automatically, 117 mean diameter, 197

calculation of, 196 planar, 167

Populations of neurons, statistical analysis of, 241

design of tests, 258 Pop-up menus, 16g, 269, 270, 272f, 275 Port, 16g, 42, 62

asynchronous, 2g, 62 Centronics, 62 configuring, 62 IEEE-488, 63 line printer, 62 parallel, 15g, 42

printer, 17g, 62 serial, 18g, 199, 42, 62

RS-232, 18g, 62, 70 Positional mode of joystick control, 93

INDEX

Positioning, with interactive devices absolute, 57 relative, 58

Positioning a cursor on a video screen, 278 Potentiometers, 16g, 60, 61

on microscope stage, 104 Power of a statistical test, 258, 259 Power supply, 64f, 65

transformer, constant-voltage, 341, 345 Presentation of output, 281 Presynaptic dendrites, 358 Primary antibody, 363 Primary colors, 287f, 302, 303, 303f Primary field, 17g, 53f Principal-axes analysis, 253, 254f Principal axis of a structure, 199 Printed circuit boards, 63 Printer, 17g, 49

dot matrix, 8g, 49, 5Of, 165 for printing images, 130

golf-ball, 49 laser, 12g, 49, 50, 5lf, 165

binary device, 190, 191 dithering to achieve gray scale, 190, 191 plots on, 190

method of generation, 190 for raster hard copy, 190 speed of, 191

letter quality, 12g, 49 spatial resolution of, 49

Printer port, 15g, 17g, 62 Processing speed, 339, 365f, 366 Processor, 336

array, 2g Productivity in writing software, 81, 83 Professional programmers, cost of, 85 Profit, short term, 86 Program, 17g, 39, 83, 83f; see also Software

author's proximity to user, 83 bug, 4g, 63, 74 on a computer, 71 crash, 6g, 281 customer telephone support, 83 debugging, 7g, 74 documentation of, 267, 282

need for, 282 user manuals, 282

cost of, 283 for reference details, 283 for strategy, 283 tutorials, 283

end user of, 8g executable file, 73, 73f execution of, 72 feedback, need for quick response, 268 flexibility, 84

vs learning time, 273 interacting with, 268 library, 73 module,13g

Program (cant. ) product, 83, 83f, 84, 266 quick and dirty, 84 real time, 18g responses of. 266 run file, 73 running a, 73 save file, 73 self,84 source files, 72, 80f

translation of, 72, 73f, 76 subroutines, 13g, 199

libraries of, 282 system, 17g, 83f, 84 system product, 83f, 84 user, 21g variable, 21g, 76

473

Programmable read-only memory, 17g; see also PROM

Programmed input/output, 17g; see also PIO Programmers, 17g

background of, 85 cost of professionals, 85 hiring personnel, 84, 86 knowledge of the program's user, 267, 268 students as, quality of, 85

Programming, Ig, 17g, 72 custom, 82 defming of program, 84 to duplicate the human visual system, 373 effort required, 265 fmding personnel, 86 human factors engineering in, 266 parameters

changing and maintaining, 276 setting of, 275, 276

principles of closure, 268 continuity, preservation of

concentrational, 276 tactile, 145, 276, 277 visual, 145, 270, 276

feedback immediate, 274 from a program, 268 during tracing, 89 visual, 277, 278

know the user, 84, 271, 273 for novice user, 84 obvious next step, 268 tactile continuity preservation, 145, 276, 277 visual continuity preservation, 145, 270, 276

toolboxes for, 282 typing, elimination of, 275 utility programs, 74

Programming languages: see Languages Programming Language/I: see PLiI Projecting microscope, 1I3f, 1I5f Projection

of displayed structures

474

Projection (cont.) of displayed structures (cont. )

disadvantages of, 241, 242f orthographic, 170, 171f, 172

flaws of, 172 of trees, 248 value of, 172

perspective, 17lf one-point, 170

of neurons, fan-in, 249 onto two-dimensional screens, 170

Prolactin immunoreactivity, 370 Prompting of user

for data, 272 for parameter ranges, 280

Proportional sum of absolute deviations, 225, 226f, 228, 232; see also PSAD

for multifurcating trees, 234 of the soma, 235

Proximity of program's author to user, 83 Pseudocolor, 17g, 345

display, 288, 346, 347f, 367 exaggerating a small difference, 330 mapping, 303, 303f, 304f

Puck, 6g, 17g, 57, 57f use in tracing, 276

Pull-down menu, 17g, 269, 270, 27lf, 275 Purchasing a computer, 68

testing program on own data, 85 think "software first," 85 vendor, 86

dilemma of, 86

Q-bus, 68 Quality reduction by televising, 130, 13lf Quantex Corporation, 415 Quantitative immunocytochemistry, 334, 337, 344,

360, 365f, 367, 369, 370 Quantitative receptor autoradiography, 367, 368 Quantization of image into pixels, 146; see also

Image, digitization into pixels Quarter-hexant region of a cube, 252 Quick and dirty programs, 84

Rand M Biometrics, Inc., 416 RAM, 17g, 40, 45; see also Random access,

memory disk, 17g

ROB,18g color coding, 288 input, 18g

ROB/TIL monitor, 17g ROI, 18g, 368; see also Region of Interest ROM, 18g, 45, 75, 80; see also Read-only memory RS, 18g, 62; see also IEEE; Recommended

standards RS-170 composite video, 18g, 297

pedestal voltage, 297 television standard, 288 video component, 297

RS-232, 18g, 70 port, 62

RS-232C: see RS-232 RS-330 television standard, 18g, 288 RT-ll,75 Radial distance from the soma, 200 Radioimmunoassay, 370 Radioligand work, standards for, 367 Radius of curvature, 161, 162f

ftltering, 161, 162f justification for, 161, 162f

Rall's ratio versus branch order, 211f calculation of, 207, 210f

Random access, 45 data files, 123, 123f, 124 memory, 17g, 40

Ranking in statistical tests, 261 Raster, 17g, 52

displays aliasing problem, 182, 183f

INDEX

of anatomical structures, techniques, 192 cost of, 183f, 188, 189 dynamic, cost of, 189 enriched, 187, 187f, 188 hidden-surface removal, 184f image generation, 184 realism of, 181, 182f, 184, 184f, 186f, 187,

187f, 188f resolution, 183 serial section reconstruction, 183f, 184 spatial resolution, 188 staircase effect, 55, 160, 160f storage on disk, 188 storage requirements, 177 surface-filled, 184, 184f, 186, 186f systems, 52, 54, 165, 167 tiling, 184 use during tracing, 103

Rats BALB/cJ,370 CBA/J,370 locomotor activity of, 370

Reaction agents, 362 product, 333

Read-only memory, 18g, 45, 74, 75, 80 Reagent dilution, 363 Real time, 18g Reassembly of serial sections, 149 Receptive field of a neuron, 197 Receptor density measurements, software for, 367 Recommended standards, 18g, 62 Reconstruction, 36; see also Serial section

reconstruction; Neuron tracing from EM photographs, 112 enriched view of, 109 intermediate computations in, 149 of neurons, 87 of neurons, time required, 255 problems in automation, 373 of serial sections, 109 of spines, 200f thin vs thick section, 113

INDEX

Recording structures in their environment, 89 Red, green, blue, 18g; see also RGB Reducing points in the data base, 160 Reference gray level, 339 Reflected light microscope, disadvantages in neuron

tracing, 385 Refresh, 18g

of display, 177 hardware in raster displays, 181

Region of growth of a neuron: see Region of influence of a neuron

Region of influence of a neuron, 197, 202, 203f Region of interest, 18g, 138, 140, 14lf, 368; see

also ROI area of, 140, 197, 198f volume of, 197

Relative positioning, 58 Rendering displays, 165, 167 Renumbering of trees, 159f, 163 Reordering of trees: see Renumbering of trees Repositioning cursor to next frame, 134 Rescaling images

difficulties of, 326f using Fourier transforms, 326

Reserpine, 370 Resolution

of image processing systems, 366 of passive stage, 105 spatial, 338, 365f

of an image, 288 of image-sensing devices, 336 of scanner, 334

Responses of computer program, 266 Reticule, 1I8

cross-hairs used as cursor, 105 Return to branchpoint from ending, 134 Reverse Fourier transform, 326 Road to Pt. Reyes, 182f Robust, 18g

characteristic of statistical tests, 261 Root directory, 18g Root segment, 18g

diameter correlated with other measures, 244 Rotating-drum scanner, 334 Rotating images

difficulties of, 326f using Fourier transforms, 326

Rotation, smooth: see Smooth rotation Rotational alignment of tissue sections, 154, ISS

automatic techniques, 155 rotatable specimen holder, use of, 155 semiautomatic after tracing, 155, 156f using artificial landmarks, ISS using natural landmarks, ISS using tissue edge, 155

Run file, 73 Run-length encoding, 122, 122f

of images, 295 Running a program, 73

SAS,79 SECAM, 199

475

SIT, 336; see also Silicon-intensifier target SIN ratio, 18g, 336; see also Signal-to-noise ratio SPEX Industries, Inc., 418, 419f SYSTAT,79 Sample sizes in statistical tests, 258, 259, 259t,

260, 261t Sampling levels for statistical comparisons, 257

cost of, 260 Sarastro, Inc., 416, 417f Save file, 73 Scan line, 18g Scanners, 334, 367

drum, 8g, 334 flatbed, 9g, 334 image, 366 speed of, 338 use of linear diode arrays, 293

Scanning stage, 18g cost of, 292 time to acquire an image, 292

Schematic diagram of a neuron, 206, 209f Scientific notation, 44 Scintillation counts, 371 Screen cursor, 269 Scripting, 13g, 199, 271; see also Macro

file, 73 Scroll, 199 Secondary antibody, 362 Section alignment: see Alignment, of serial sections Sectioning plane, choice of, 236, 244

to help statistical comparisons, 256, 257 Sections: see Tissue Sector, 199 Segment, 199

root, 18g Segmental growth model, 199, 221, 222f, 224 Segmentation

of cells, 358 of an image, 315

Selection of dots by name, 102 of laboratory software, 86 of trees from data base, 10 I

Semiautomatic neuron tracing, see also Neuron tracing

history, 107 need for, 241 use of in morphology, 107

Semiautomatic tracing, 87, 89; see also Tracing of serial sections, 113 using video, 133, 133f

Sensing movement in an image, 61, 312 Sensitivity of image-sensing devices, 336 Sequential data files, 123f; see also Serial data files Serial communications, 70

data bits, 6g, 62 with null modem, 63 parity, 16g, 62

bit, 62 even, 16g, 62 odd, 16g, 62

RS-232, 18g, 62, 70

476

Serial communications (cont.) stop bits, 199, 63 with telephone modem, 13g, 51

Serial data files, 123, 123f, 124 Serial number, 199 Serial port, 18g, 199, 42, 62 Serial section reconstruction, 109, llOf; see also

Displays; Tracing alignment of sections, 119, 154

automatic, history of, 126, 127 computer-assisted, 120 cumulative errors, 119 with pin holes, 120 rotational, 154, 155

automatic techniques, 155 rotatable specimen holder, use of, 155 semiautomatic after tracing, 155, 156f using artificial landmarks, 155 using natural landmarks, 155 using tissue edge, 155

use of 35-mm slides, 119 using cut tissue edge, 120 using fiducial marks, 120, 155

analysis of structures numeric summaries, 137f, 193, 194, 194f,

195 use in anatomy, 126 changing point parameters, 124 coordinate system, 112 correcting errors, 124 cursor for, 113

cross-hairs reticule, 105 optically mixed with microscope image, 87 presented in microscope, 95f

data editing, 124 entering by typing, 126 organization, 123, 123f

displays in, 125 raster, 183f, 184

done directly from microscope, 118 drawings of tissue sections, 113 file conversion, 124 hidden-line removal in, 174, 175, 187 history of, 110, 126 identification of points, 124 input of Z value, 117 inserting points, 125 justification, 109 locating structures with dots, 117 microtome accuracy, 150 models, 33f, 34f, 35, 110, l1lf naming structures, 119 optical encoder system on stage, 70, 104, 105 photographs of sections, 113 photographs of tissue sections, tracing from, 113 point deleting, 124 purpose, 112 reassembly of sections, 149 reducing points in the data base, 160 reviews, 110, 127

Serial section reconstruction (cont. ) sectioning of tissue

optically, 15g, 113,327, 328f physically, 113

semiautomatic tracing, 113 shear diagrams, Ill, 112f statistical summarizations, 125 storage of data, 117

linked list, 123f, 124 techniques, III types of points, 117

close, 122 dot, 122 draw, 122 move, 122

use of plotting microscope for input, 125 Serotonin (5-HT), 352f, 353f, 369 Shaded displays, 165 Shading corrections

algorithms for, 339, 34Of, 341 errors in, 340

Shaft encoders, 61

INDEX

Shape factor, 344, 355; see also Form factor Sharpening an image, 346

from out-of focus, 322f, 325f Shear diagrams of serial section reconstructions,

111,112f Sholl, D. A., 35

analysis of neurons, 215, 216, 216f concentric-spheres analysis, 35f, 208, 212f, 247

including area correction, 208 schematic diagram, 36f, 206

Short-term profit, 86 Signal-to-noise ratio, 199, 336

improvements in video convolution, 308f exponentially weighted temporal averaging,

305, 307, 307f kernel,308f mask,308f real-time averaging, 307 spatial low-pass filter, 308f spatial smoothing, 308f techniques for, 305 temporal averaging, 305, 306f, 342f

hardware for, 307 limitations on, 305, 307f

Significance level of a statistical test, 259, 259t Silicon-intensifier target, 336 Silicon wafer, 63 Silver deposit, 99 Silver grain counting, 143 Single-diode densitometer, 292 Single-sided disk, 199 Single user operating system, 75 Size of company, 85 Skeletonization, 358

of an image, 355 Sketchpad, 165 Slicing tissue to minimize merging: see Sectioning

plane, choice of

INDEX

Slide origin, 199, 94 Slides, 35-mm, of tissue, 113

use in section alignment, 119 Slot, 199

expansion, 8g Smooth rotation, 158, 167

cost of, 168 coupled with kinesthesia, 167 of vector displays, 178

Smoothing: see Filters, low-pass of facet boundaries, 186f, 187 of an image, smoothing, 308f

comparison of techniques, 310f a neuron, 160, 160f

Software, 199, 39, 71; see also Program already-written, 85 applications, 74, 78, 265 author of, 83 availability of, 47 for binary operations, 366, 367 bug, 4g, 63, 74 commercially available, 265 compatibility, 5g, 66, 69

upward,21g cost of, 81

vs hardware, 71, 82 vs level, 82

crash, 6g, 281 debugging, 7g, 74 for drawing

MacPaint, 67, 117 for gel electrophoresis, 366 handler, 109 for image processing, 296 inherent problems in, 83 investment in, 82 for laboratory, selection of, 86 level of

high, 109, 77, 366 proprietary, 81

low, 13g,77 for managing journal references, 79 mass production of, 82 module, 13g for neuron tracing, review, 107 for office

electronic mail, 79 electronic yellow pages, 79 general purpose, 79 spreadsheet, 78 text editors, 74, 77, 78 word processors, 78

productivity in writing, 81, 83 for quantitative immunocytochemistry, 334 for receptor density measurements, 367 spreadsheets, 78

Lotus 1-2-3, 79, 279 statistical

SAS, 79 SYSTAT,79

support for. 83

Software (cant. )

system assembler, 2g, 76, 77 compiler, 5g, 72, 77 interpreter, Ilg, 77 linker, 73, 73f

task, how to accomplish, 84 text editing: see Word-processors toolboxes, 20g, 84,282, 296 user friendly, 21g, 266, 267f user module, 21g word-processing, 78

MacWrite, 67 Solid angle of a sphere, 248, 249f Solid-state camera, 336, 365f Soma

cross-sectional area of, 195, 243 plots with filled, 190f, 19lf size of

correlated with other measures, 242, 243 measurements of, 242

surface area of, 243 volume of, 243

obtaining accurate measures of, 242 Soma continuation point, 95f, 102 Soma outline end, 96, 96f, 102 Soma outline start, 95, 102 Source files, 72, 80f Sources of software, 85 Southern Micro Instmments, Inc., 417 Spatial

averaging of an image, 308f calibration, 345

477

domain, 321, 325 filters, 288

filters, 101, 117, 134, 160, 16lf, 277 for dots, 117 logical operations, 310

orientation of trees, 247 resolution, 338, 365f

of an image, 288 of image-sensing devices, 336 of scanner, 334

smoothing of an image, 308f comparison of techniques, 310f

Special point types, selected from perimeter menu, 134

Spheres solid angle of, 248, 249f neuron analysis by: see Sholl, D. A.

Spines, 36, 99; see also Dendrites base of, 99 density of, 199 distribution of, 20lf types of, 200, 200f

Spreadsheet, 78 Stacking images by image processing, 327, 328f Stage, microscope: see Microscope, stage Stage micrometer, 345 Stage, scanning, 18g Stage, stepping, 199

478

Stage movement during mapping, 101 Staining, 27

loss of, 99 Staircase effect, 55, 160, l6Of; see also Aliasing Standards, 364

of computer comparisons, 375 curve, 371 of optical density versus concentration, 364, 365f step-wedge, 364 topological diameter of a tree, 239

Stand, copy, 130 Statistical analysis, 28, 79; see also Neurons,

analysis of cost of samples, 260 of neuronal populations, 241, 257 parametric and nonparametric testing, 260, 261 plots of, 190 power of, 258, 259 ranking in, 261 robust characteristics of, l8g, 261 sample sizes in, 258, 259, 259t, 260, 26lt sampling levels for comparisons, 257

cost of, 260 sectioning tissue to help comparisons, 256, 257 significance level of, 259, 259t tedium in applying, 35 transformation of data, 260, 261, 262 variance, 258

Statistical software for the laboratory SAS, 79 SYSTAT,79

Statistical tests applied to topological parameters, 238

coefficient of variation, 259 components of variance, 258, 260, 26lt design of, 258 Kruskal-Wallis test, 261

Stepping motors, 199, 61 on microscope focus, 61 on microscope stage, 61 use in video digitizing, 130

Stepping stage, 199 Step-wedge standard, 364 Stereo pair displays, 38, 175, 176, 176f

aids for viewing, 176 angle between views, 176, 176f building of by image processing, 329, 329f of neurons, 242f stereopsis, 167 generation from video systems, 147

Stop bits, 199, 63 Storage of data, 278; see also Digitized images,

storage of automatic, 279 backup, 279 Bernoulli box, use of, 295 compact disks, use of, 296 compression techniques, 122, 122f, 123f computer representation of traced data, 95 of digitized images, 295, 336, 337 on disk, 161,278

Storage of data (cont.) file access, types of, 75 flexibility in, 279 format of, 279 frequency of, 162, 279 how to store on disk, 162 linked list, 123f, 124 Lotus format, 279 on magnetic tape, 45, 46 multiuser access to, 75 programmed input/output, 16g, 17g PROM,17g RAM, 17g, 40, 45

disk, 17g ROM, 18g, 45, 74, 75, 80

programmable, 17g run-length encoding, 122, 122f

of images, 295 techniques for, 161, 162 of traced data, 102 tractable, 36, 87 units of

byte, 4g, 43 kilobytes, 12g, 45 gigabyte, 45 megabytes, 13g, 45 word, 43

user-invoked, 279 on VCR, 296 for vector displays, 177 when to store on disk, 162 on WORM, 296

Strahler ordering, 230f, 236 Stria terminalis, 370 Structures

automatic tracing of, 132 locating in the tissue, 102, 103f

using a video system, 135, 138f names of, 122 major axis of, 199, 199f mathematical summarization of, 193 measurements of fine details, 146 plots of, three-dimensional, 189 principal axis of, 199

INDEX

recording structures in their environment, 89 Student progammers, quality of, 85 Student t-test, use in dendritic density comparisons,

255 Stylus, 199 Submenus, 199, 270, 270f Subprogram: see Subroutines Subroutines, 13g, 199

libraries of, 282 value of in applications programming, 282

Substantia inominata, 370 Substantia nigra, 370 Subtraction of images, 329

background, 3g Subtractive color mixing, 302, 303 Subtrees, 218f

topological rotation of, 218n

INDEX

Sum of centrifugal orders, 228, 230 Superior colliculus, 347f, 352f, 353f, 369, 370 Support, customer telephone, 83 Surface area of region of influence, 197 Surface-filled displays, facets, 184, 184f, 185, 186,

186f Surrounder test, 187

in hidden-line removal, 174, 175 Swellings, 36

versus branch order, 202f distribution of, 202f

Symmetry, branching, 198 Synaptic terminal, 360, 36lf Synchronization, video, 20g

sync generator, 54 System,20g

application, 366 closed loop, 5g component, 366 open loop, 14g of programs, 17g responsibility for, 85 software, 74, 76; see also Software turnkey, 21g, 85, 366

TIL,21g input monitor, 21g

Tablet, data: see Data tablet Tactile continuity, 145

preservation of, 276, 277 Tags, 95, 97, 194 Tape, magnetic, 45, 46 Tapering

of a branch segment, 206, 207f of a dendrite, 243 ratio, 206, 207f

versus branch order, 208f Tasks, bounded, 67 Technology Resources, Inc., 419, 420f Tedium in statistical summaries, 35 Telephone

computer use with modem, 13g, 51, 79 customer support over, 83 data transmission over wires, 51

Televised image of microscopic data, 129, 130 Television, 288; see also Video

aspect ratio, 2g camera, 53, 130, 292, 293, 335f, 337

accuracy in measuring gray values, 145 automatic parameter setting, 293 bum-in of, 4g, 294 chalnicon tube, 293, 336 cost of, 294 dark current, 343 deflection of beam, 7g electronic circuitry, 293 gain and offset, 345 gamma, 109, 293

correction circuitry for, 293 intensified silicon-intensifier target, 306f intensity range, 294

Television (cont. ) camera (cont.)

ISIT,306f lens, C-mount, 4g linearity of response, 293 newvicon tube, 293, 336, 360 plurnbicon tube, 293 scan line, 18g sensitivity, 293, 338, 341, 345 signal-to-noise ratio, 293 silicon-intensifier target, 294, 336 SIT, 294, 336 solid-state, 336, 365f spatial resolution, 293 tube, 4g, 53, 293, 339 vidicon tube, 293, 336, 338, 365f

closed-circuit, 4g, 5g high-density, 109, 288

479

monitors, 130, 288, 334, 335f, 337, 345, 357f, 358, 365f, 366, 367

composite video input, 294 cost of, 294 deflection of beam, 7g input

ROB, 18g, 294 ROB/TIL, 17g TIL, 294

monochrome and color, 294 multisync, 14g spatial resolution, 294 underscanned, 21g, 294

quality reduction by, 130, l3lf standards

European, 288 CCIR, 4g, 288 NTSC, 14g, 288 PAL, 15g, 288 RS-170, 18g, 297 RS-330, 18g, 288 SECAM,19g

Template matching, 381 Temporal variability, 339

long-term, 341, 342f short-term, 341

Tennis tournament diagram, 206, 209f; see also Sholl, D. A., schematic diagram

Ten-to-one rule of vectors, 150, 15lf Terminals, 20g

axons,358 clustering of

Poisson distribution of, 213 computer, 20g, 42

beeping of, 280 interrupt from, 12g polling of, 16g scrolling of, 199

growth model, 20g, 221, 223f, 224 segment, 20g

measures of, 245, 246t synaptic, 360, 36lf

Tesseling, 184

480

Testing program on own data, 85 Testosterone, 370, 371 Tests of statistical significance, 258 Text editors, 74, 77, 78; see also Word processors Thickness measurements without circular cursor, 105 Thickness of tissue, 112 Think "software first," 85 Thinning operator, 336, 355, 366, 369

results of, 352f, 353f Thin vs thick section reconstruction, 113 Third-party software for image processing, 367 Three-dimensional displays, 165

goals, 165 of neurons, 242f with varifocal mirror, 192

Three-dimensional drawing, 38 Three-dimensional images, building of, 327, 328f Three-dimensional principal component analysis,

253, 254f Three-dimensional tracing using video, 135 Threshold, 20g

applied to an image, 310, 336 local, 315

real-time, 367 Tiling, 184

effect of, 185f Time-based point entry during tracing, 277 Time sharing, 48, 75

time slice in, 75 Tissue

contrast, 27 cut by microtome, 101 origin, 20g, 94 photographs of, 113 sectioning, see also Serial section reconstruction

optical, 15g, 113, 327, 328f physical, 113 plane, choice of, 244

to help statistical comparisons, 256, 257 shrinkage, 150

correction for, 149 effects on statistical analysis, 263

silver deposits in, 99 35-mm slides of, 113 staining, 27

loss of, 99 thickness of, 112 wrinkling, 150, 151, 151f

correction for, 149, 151, 152f Toolboxes, 20g, 84, 282

in user interface, 273 for image processing, 296

Top artificial end, 99 Topological analysis of neurons, 20g, 215

asymmetry of a tree, 225 muItifurcating, 234, 235

center of mass, 228 centrifugal order

mean, 228, 230, 232 sum, 228, 230

characteristics of neurons, 216

INDEX

Topological analysis of neurons (cant.) classification of trees, 217, 220t, 221, 222f, 233

by class number, 219 by PSAD values, 225

degree, 7g of subtree pairs, 221 of trees, 217, 218, 219, 219f, 220t, 228, 232,

237 of a tree segment, 230

description of trees, 20g, 217, 218f diameter

of root segment, 244 standardized, 239 of a tree, 231, 239

muItifurcating, 235 distance from the root, 228 justification for, 215 mean degree of a tree, 230, 232 mean PSAD, 225, 226f, 228, 232, 233

of muItifurcating trees, 234 measures of trees, 227t, 237, 238

correlation of, 233, 233t, 234t, 238 review of, 238, 239

muItifurcating trees, 225, 234 parameters of trees, 221

testing with Chi-square test, 221 partitions of trees

first-order, 219, 219f, 220t, 221, 222f, 223, 223f, 233, 238

path length of trees, 20g, 218f, 228 maximal, 231 total, 228, 230

proportional sum of absolute deviations, 225, 226f, 228, 232; see also PSAD

for multifurcating trees, 234 of the soma, 235

by PSAD, 225, 226f, 228, 232 size of a tree, 20g, 217 of the soma, 235 structure of a tree, 217 subtrees, 218f

rotation of, 218n summarization, 193 symmetry of branching, 198 tree types, 20g, 218, 218n, 219f, 237

distribution of, 219 vertex analysis, 228

ratio of, 228, 232 Top tree origin, 99 Tortuosity, 195, 195f Total dendritic length, 243 Total path length of a tree, 228, 230 Tracing, see also Neuron tracing; Serial section

reconstruction basic operations, 277 changing focus during, 99f close point, 122 controling with interactive devices, 276 coordinate systems for, 94, 94f cursor for

cross-hairs reticule, 105

INDEX

Tracing (cont.) cursor for (cont. )

in microscope, 95f moving over stationary image, 134

dendrites, 96 distance-based point entry, 277 distinguishing among structures, 89

use during tracing, 29f, 3Of, 31, 1I6f drawings of tissue sections, 113 drawing tube, 31; see also Camera lucida feedback during, 89, 90, 1I4f, 1I5f, 134 laminae, 356, 358, 359, 369 with MacPaint, 67, 117 methods of point entry, 277 optical encoder system on stage, 70 with pantograph, 15g, 31, 32f, 33f, 125 paper, use in section alignment, 119, 120f with passive microscope stage, 104

resolution of, 105 photographs of tissue sections, 113 semiautomatic, 87, 89 soma outlines, 94

using a video system, 135, 136f structure outlines

automatically, 132 using a video system, 135, 137f

three-dimensional, using video, 135 time-based point entry, 277 trees continued in adjacent sections, 99 use of colors, 119 use of icons, 119 use of keypad, 9lf, 94, 95 use of perimeter menu during tracing, 135 use of puck, 276 using joystick to control, 92, 93, 93f, 105 using the microscope stage, 277 using a video image, 278 vector displays, advantages of, 103 without computer overlay, 105 writing coordinates on paper, 106

Track,20g Trackball, 20g, 60, 60f

used to control a microscope stage, 277 Tractable, 36, 87 Transformation of data in statistical testing, 260,

261,262 Transformer, constant-voltage, 341, 345 Transistor-transistor logic, 21g; see also TTL Translation, 72, 76

of a source file, 73f Transmittance, 21g, 338 Transmitters, 369, 370

pathways of, 358 Transparent surfaces, 187, 187f Trees, see also Dendrites, Neurons

ambilateral types, 2g, 218n attachments to, 100f, 152, 153f, 154, 156f binary, 3g, 157, 225, 232

characteristics, 157, 158f storage of, 158f

botanical growth vs dendritic growth, 214

Trees (cont.) connectivity pattern of, 216 elements of, 218f growth models of

neuronal, 217 physical, 32, 33f, 34f, 35 segmental, 199, 221, 222f, 224 terminal, 20g

incomplete analysis of, 217, 236, 237 measurements of, 244 types of, 237

measurements of, 27, 194f review of, 263

multifurcating, 225, 234 origins of, 21g patterns of branching, 209f principal axes of, 17g principal planes of, 17g renumbering of, 159f, 163 segment, 199

intermediate, II g root, 18g

481

diameter correlated with other measures, 244 spatial orientation of, 247 subtrees, 218f

topological rotation of, 218n topological classification of, 217, 220t, 221,

222f, 233; see also Topology by class number, 219 by PSAD values, 225 vertex analysis, 228

ratio of, 228, 232 trifurcations, 4g, 21g, 99, 234

frequency of occurrence, 234 Triangulating, 184 Trifurcations, 4g, 21g, 99, 234

frequency of occurrence, 234 True color image processing systems, 295 Tube

camera,4g cathode ray, 4g; see also CRT

Turnkey system, 21g, 85, 366 Two-bus computer, 48 Two's complement representation, 43 Typing, elimination of, 275 Tyrosine hydroxylase, 369, 370

antibodies to, 363

UNC Neuron tracing system, 90 UNIX, 76, 79 U.S. Patent Office, 79 Underscan, 21g Undo command, 274 Uneven illumination in an image, corrections for,

312 Unibus, 68 Universal Imaging Corporation, 420, 42lf, 422f Unwanted refraction, 150, 150f, 163 Upward compatibility, 21g Use of perimeter menu during tracing, 135

482

User,21g User-computer dialogue, 265, 268; see also

Computer-user interface User friendly, 21g, 266, 267f User interace, 265, 266; see also Computer-user

interface; Errors coping with errors, 280 cost of, 266, 268 design principles, 266, 267, 267f, 273, 276 direct manipulation systems, 273 types of, 268 value of, 266, 267f, 268

User manuals, 282 cost of, 283 for reference details, 283 for strategy, 283 tutorials, 283

User module, 21g Utility programs, 74

VAX, 68 VCR, to store digitized images, 296

advantages and disadvantages, 296 spatial resolution, 296

VDT: see Video, display terminal VGA, 21g, 47, 66, 288 VME bus, 22g, 67 Variable, 21g, 76 Variable-diameter cursor, 93, 103

use of, 97f Variance in statistical tests, 258 Varicosity, 99; see also Swellings Varifocal mirror, 192 Vector-based image, 129, 130, 373

conversion from pixel-based, 373 of serial section data, 123 of structures, 122, 134

Vector to a dendritic centroid, 25lf Vector displays, 52, 55, 165, 167

advantages during tracing, 103 color, 180, 181

beam penetration, 181 cost of, 180 RGB,180

monochrome, 179 storage requirements, 177

Vector representation of data: see Vector-based image

Vendor, 86 dilemma of, 86

Versabus Module European, 67; see also VME bus Vertex analysis, 228

ratio of, 228, 232 Vertical gradient extraction filters, 320f Vertical sync pulses, 21g, 53 Video, 21g; see also Television

analog adjustments, limitations on, 298, 299f aspect ratio, 2g automation of mundane tasks, 145 blooming, 298, 299f to build stereo pairs, 147

Video (cont.) color

information loss, 146 intensity, 303 saturation, 303 space, 303, 303f, 304f

composite, 6g, 53 contrast, 6g cursor, mixing with image, 129 digitizer, 21g

board,54 column, 70 use with stepping motors, 130

display terminal, 272 enhancement

advantages of, 321 hardware for, 285 techniques for, 285

gain and offset, 297

INDEX

effects on spatial resolution, 297, 298, 298f, 299f

graphics array, 21g, 288; see also VGA gray scale

color transformations, 302 encoding, 299, 300f, 30lf

using LUT, 299, 302 resolution, 299, 300f, 30lf transformations, 302

digital, 299, 300f, 30lf gamma correction, 302 histogram equalization, 302 transmittance-to-density, 302

input, 292 advantages and disadvantages, 145, 146 of point types, 136 techniques, 129 of thickness, 135 using common equipment, 145

microscopy, 22g review of, 331

pedestal voltage, 297 raster

interlaced, 53, 53f interlace field, Ilg, 53f one-to-one, 14g primary field, 17g, 53f

noninterlaced, 14g RGB, 18g

color coding, 288 RS-170 standard, 18g, 288, 297

pedestal voltage, 297 video component, 297

RS-330 standard, 18g, 288 scan line, 18g

horizontal, 109 signal,53 signal-to-noise ratio, 199, 285, 336; see also

Signal-to-noise ratio; Video reducing noise, 305

synchronization, 20g generator of, 54

INDEX

Video (cant.) synchronization (cant.)

pulses, 53 horizontal, 109, 53 vertical, 2Ig, 53

systems for collecting anatomical data, 130 components of, 132f cost of, 146 for three-dimensional tracing, 135 for tracing, history, 146 training required, 146

unde~canning, 21g, 294 use with semiautomatic tracing, 133, 133f

Video-cassette recorder: see VCR Vidicon, 293, 338 Vidissector, llg, 21g, 376; see also Image dissector

use in automatic neuron tracing, 376f Viewing medium, 25 Vision by computer, cabilities and failures, 373 Visual continuity, 145

preservation of, 270, 276 Visual cortex, 356, 357f

areas 17 and 18, 357f Visual feedback, 143f, 144, 145, 156

in microscope, 95f, 97 during tracing, 90, 114f, 115f, 134

Visual inspection of the data base, 158 speed of, 159

Visual presentation of commands and data, 273 Volatility, 45

of memory, 22g Volleyball net algorithm to de-wrinkle, 151, 152f;

see also Tissue, wrinkling Voltage-sensitive dyes, review of use, 331 Volume

-based measurements, 196 elements of, 188, 380 of neuron, 196 of region of influence, 197

Voxel, 188, 380 -based image representation, 386

W-type cells, 360, 369 Wavelength,345 Weight

of body, 262 of brain, 262

Wildcard, 101 Wild Leitz U.S.A., Inc., 421, 423f Winchester disk, 109, 22g, 46 Windows, 270

controlling size and location with mouse, 139 for display, 169, 169f

Wireframe displays, 55f, 56f, 165 vector ve~us raster perfonnance, 189

Wollaston, W. H., 28 Wooden blocks, 34f, 35 Word,43 Word processo~, 78

MacWrite, 67 Working distance of microscope, 107

483

WORM, 296; see also Write once, read many disk drives

Wrinkling of tissue, 150, 151, 151f correction for, 151, 152f

Write once, read many disk drives, 296; see also WORM

Writing coordinates on paper during tracing, 106

Yellow pages, electronic, 79 Y-like cells, 360 Yoke,22g

Z-80 CPU, 66 Z coordinate presented in microscope, 97 Zilog Corporation, 66 Zooming, 22g, 166, 355

dynamic, with perspecitive divider, 172 static, 172