scale bar tools for microscopes

8/9/2019 Scale Bar Tools for Microscopes

1/22

/////////////////////////////////////////////// Scale Bar Tools for Microscope Collection////////////////////////////////////////////// Author: Gilles Carpentier// Faculte des Sciences et Technologies,// Universite Paris 12 Val de Marne, France.// May 2009

// documentation at the http://image.bio.methods.free.fr/ImageJ/?Scale-Bar-Tools-for-Microscopes.html// Image sample, http://rsb.info.nih.gov/ij/macros/images/myotube.tif.zip// The RGB image sample, is a composite of three microscopic images of the samefield in fluorescence mode.// The example contains a triple lableling of a differentiated mouse myogenic cell line.

// Cell culture and immunochemistry; Juliette Peltzer.// Images from the courtesy of Dr Angelica Keller. Scion CFW-1310M CCD camera mounted on an Olympus BH-2 with a

// 0.3x C-mount optical adaptor.// For more details about the cell line, contact Dr Angelica Keller at [email protected]// Faculte des Sciences et Technologies,// Universite Paris 12 Val de Marne, France.

// global variables// Check the netvar errorNetMessage ="Error: ";var urllist = "http://image.bio.methods.free.fr/ij/ijupdatetest/ListOfMacros.txt";// to check the internet access// Array containing the calibration data specific to each acquisition device:var microscope1=newArray("");

// variable for demo imagevar demoimagelink = "http://rsb.info.nih.gov/ij/macros/images/myotube.tif.zip";var demoimagelink2 = "http://image.bio.methods.free.fr/ij/ijmacro/scalebar/myotube-sc.tif";var demoimagename = "myotube.tif";var onlinedoclink = "http://image.bio.methods.free.fr/ImageJ/?Scale-Bar-Tools-for-Microscopes.html";var demoimagename2 = "myotube-sc.tif";// variable for the objectives datavar objectdata = newArray(16);var objective = newArray("no choice","Unchanged","Uncalibrated","","","","","","Other"); // list of choice deduced from objectives data

var obj="no choice",reponseUser,model="";var nomdimage ="", imageid,imageCalibid,imagex,imagey,blackmarge=0,nblinecom=3,hightnblinecom=15,hightcom=24,TimeString;var userchoices = newArray(14),pixobj,calibration ="",textcalib="",otherobjecvalue,otherobjective,unit,pixelWidth, userLenght=0,lastCustuserbar=0;var microscopeCollection="Microscope Profiles Collection",editMode=0;var pixdist=1,knowndist=0.2, scaleunit="",defaultbar=0,pixobj=1,zoom=1,otherpixdist,otherknowndistance,othermodel="",autosave=0,spacerset=1,metaset=1,scalebarset=1,infoset=1,scaleset=1,noscaleLine=0;var um = getInfo("micrometer.abbreviation"); // m

var xx = requires143d (); // check version at install timefunction requires143d() {requires("1.43d"); return 0;}

macro "Unused Tool- 1" {} // Space (empty tool icon) between native ImageJ toolsand tools of this toolset.


2/22

macro "Scale Bar Action Tool - C111D4bD4cD6bCfffD00D08D09D0aD0bD0cD0dD0eD0fD10D18D19D1aD1bD1cD1dD1eD1fD20D21D22D23D25D26D27D28D29D2aD2bD2cD2dD2eD2fD30D31D32D33D35D36D37D38D39D3aD3bD3cD3dD3eD3fD40D41D42D43D45D46D47D48D4eD4fD50D51D52D53D55D56D57D58D59D5aD5dD5eD5fD60D61D62D63D65D66D67D68D6dD6eD6fD70D71D72D73D75D76D77D78D79D7aD7bD7dD7eD7fD80D81D82D83D85D86D87D88D8dD8eD8fD90D91D92D93D95D96D97D98D9aD9bD9cD9dD9eD9fDa0Da1Da2Da3Da5Da6Da7Da8DadDaeDafDb0Db1Db2Db3Db5Db6Db7Db8DbbDbcDbdDbe

DbfDc0Dc1Dc2Dc3Dc5Dc6Dc7Dc8DcdDceDcfDd0Dd1Dd2Dd3Dd5Dd6Dd7Dd8Dd9DdaDdbDdcDddDdeDdfDe0De8De9DeaDebDecDedDeeDefDf0Df8Df9DfaDfbDfcDfdDfeDffC222D8bDabC03fD02D03D04D05D06D12D13D14D15D16D24D34D44D54D64D74D84D94Da4Db4Dc4Dd4De4Df2Df3Df4Df5Df6C89fD01D07D11D17De2De3De5De6Df1Df7C222D4aD6aD8aDaaC555D99Db9C999D5cC444Da9C999D6cD8cDacDccCbcfDe1De7C333D49D69D89DcaDcbC666D4dDc9CfffD7cDbaCbbbD5b"{

setScaleBarre ();}

macro "Extract and Edit Image Action Tool - C01538R01fdR23" {extractAndEditImage ();

}

var availableMicroProfiles = InstalledProfiles();// installed microscope profiles menu toolvar aCmds = newMenu("Available Microscope Profiles Menu Tool",availableMicroProfiles);macro "Available Microscope Profiles Menu Tool - CfffD00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD1fD20D21D22D23D24D25D26D27D28D29D2aD2bD2cD2dD2eD30D31D32D33D34D35D36D37D38D39D3aD3bD3cD3dD40D41D42D43D44D45D46D4bD4cD4dD50D51D52D53D54D55D5cD5dD60D61D62D63D64D67D68D69D70D71D72D73D77D78D79D89D8cD8dD99D9cDa0Da1Da2Da3Da4Da5Da6Da7Da8Da9DacDb0Db1Db2Db3Db4Db5Db6Db7Db8Db9DbcDbdDc0Dc1Dc2Dc3Dc4Dc5Dc6Dc7Dc8Dc9DcbDccDcdDceDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdaDdbDdcDddDdeDdfDe0De1De2De3De4De5De6De7De8De9DeaDebDecDedDeeDefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC38fD2fD3eD3fD48D49D4aD4eD4fD56D57D

58D59D5aD5bD5eD5fD66D6aD6bD6cD6dD6fD75D76D7aD7bD7cD7dD7fD80D81D82D83D84D85D86D87D88D8fD90D98D9fC25fD74C24fD6eD7eD8eD91D92D96D9aD9eDaaDaeC37fD47D65D8aD8bD93D94D95D97D9bD9dDabDadDafDbbDbfC32fDbaDbeDca"{

cmd = getArgument();if (cmd!="-" && cmd !="No microscope profile found" && cmd != "Record th

is tool into the \"toolsets\" folder, to use this menu tool." ) {var microscope1=GetArrayFromProfile(cmd);

}}

var mCmds = newMenu("Microscope Profiles Manager Menu Tool",newArray("Get Current Microscope Profile Infos","Get Meta-Label","Get Meta-Infos","-","Create a New

Microscope Profile","Edit & Modify a Microscope Profile","-","Erase a MicroscopeProfile","Restore a Microscope Profile from a Scaled Image","-","Update the Microscope Profiles Menu"));macro "Microscope Profiles Manager Menu Tool - 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

D9fDafDbfDcfDdfCeeeD36D37D49D5cD79D9cDacDdaCaaaD65D91D98Da5Da8Db6Dc5Dd5"{cmd = getArgument();if (cmd!="-" && cmd == "Get Current Microscope Profile Infos") {


3/22

infos=testGetArrayFromProfile();if (infos != "" ) {print("\\Clear");print(infos);} else {exit ("

No microscope profile selected");}}if (cmd!="-" && cmd == "Create a New Microscope Profile") editMicProfile

("new");if (cmd!="-" && cmd == "Edit & Modify a Microscope Profile") editMicProf

ile ("edit");if (cmd!="-" && cmd == "Restore a Microscope Profile from a Scaled Image

") testSaveaProfile ();if (cmd!="-" && cmd == "Erase a Microscope Profile") {editMode=1; rmProf

FromProfileCat (); }if (cmd!="-" && cmd == "Get Meta-Label") {

metafromima=getMetaLabel ();if (metafromima != "") {print("\\Clear");print ("Metadata of the

Image Title\:");print (getMetaLabel ());}if (metafromima == "") showMessage ("No metadata label available

in this image");}

if (cmd!="-" && cmd == "Get Meta-Infos") {metafromima=getMetaInfosIma ();if (metafromima != "") {print("\\Clear");print ("Metadata Infos

Concerning the Image\:");print (getMetaInfosIma ());}metafromprof=getMetaInfosMic ();if (metafromprof != "") {print ("Metadata Concerning the Microsc

ope Profile\:");print (getMetaInfosMic ());}if (metafromima == "" && metafromima =="") showMessage ("No meta

data infos available in this image");}if (cmd!="-" && cmd == "Update the Microscope Profiles Menu") UpdateProf

ileList();if (cmd!="-") {if (isOpen("Log")) selectWindow ("Log");}

}

var dCmds = newMenu("On Line Documentation & Demo Menu Tool",newArray ("Open OnLine Documentation","Download Unscaled Sample Image","Download a Scaled Sample Image","-","Install a Demo Microscope Profiles Set"));macro "On Line Documentation & Demo Menu Tool - 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

D53D54D55D56D57D58D59D5aD5bD5cD5dD5eD5fCa7fD00Cfd0D41D4fC444D95DbaDc9C0ffD21D2fC4f6D30CfffD7bCf88D62D63D64D65D6bD6cCeeeD72D73D74DabDbbDccDd8Cf89D6dC666Da7C84fD02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eC333D86D87D8aD99D9cDb9DbcCaaaD8eDa1Dc3Dc4Dc5Dc6CeddD76Cf89D61D66D6aD6eD6fC222DadDcdC48fD10Cfd4D40C4ffD20CaaaDacDcaDddCfaaD60C555Da2C73fD0fC333D9bDa3Da9Db1C999D7dCdddD7aD83Da8Dc7CbbbDb8C111D9aDb7CaaaD8bCf99D67D68D69C777D8cDaaCdeeD82D85C999DafCdddDd9C766D79C555DaeC999D78CcccD7eD94C888D9eC777DbfC666Db0Ca99D77"{

cmd = getArgument();

if (cmd!="-" && cmd == "Open On Line Documentation") {netTest ();doc ();

}

if (cmd!="-" && cmd == "Download Unscaled Sample Image") {OpenImageLink(demoimagelink,demoimagename,1);

}


4/22

if (cmd!="-" && cmd == "Download a Scaled Sample Image") {OpenImageLink(demoimagelink2,demoimagename2,1);

}if (cmd!="-" && cmd == "Install a Demo Microscope Profiles Set") instalD

emoCollection ();}

// click right menu// menu popup summering most used commands of the toolset (click right)var pmCmds = newMenu("Popup Menu", newArray("Scale Bar","-","Extract and Edit Image","About \"Scale Bar Tools for Microscopes\""));

// click right menu, (ctrl click)macro "Popup Menu" {

cmd = getArgument();if (cmd !="-" && cmd =="Scale Bar") {setScaleBarre ();}if (cmd !="-" && cmd =="Extract and Edit Image") {extractAndEditImage ()

;}if (cmd !="-" && cmd =="About \"Scale Bar Tools for Microscopes\"") {ab

outTheTools ();}}

macro "About \"Scale Bar Tools for Microscopes\" Action Tool - 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

5aD5bD5cD5dD69D6aD6cD9aDa9DabDacC999D0aD41DddDf6CdddD1dD2eD9eDb0C888D06D4eD6fD9fDf9CcbdD54D71D98Dc3Ca9dD17D19Dd4De6C000D74D79D95CcafDd5Dd6De8CedfD62D72D92C889D51Db1DbeCedfD53D63Da2CdcdD6eC777D8fDf8CdcfD43D44Db3Dc5CbadD2bD33C99aD23De4C545D89Da6CcbfD27Dd7CbabD61CedfD82DaaC98aD3dCdceD4dD8a" {

aboutTheTools ();}

function aboutTheTools () {requires("1.42k");about="------------------------ \"Scale Bar Tools for Microscopes\" ----

----------------------\n";about= about+"The \"Scale Bar Tools for Microscopes\" allows drawing of

scale bars in image margins, for";about= about+"\n several microscopes profiles stored on the computer. Italso allows calibration of images, and";

about= about+"\n keeps set informations in metadata. The integrity of the image area is so preserved, and margin";

about= about+"\n can be removed by a single click.";about=about + "\n-------------------------------------------------------

--------------------------";about= about+"\nInstallation: the tools file has to be stored in the \"I

mageJ\/macros\/toolset\" repertory";about=about + "\n-------------------------------------------------------

--------------------------";about= about+"\nShort documentation:";

about=about+"\n";about= about+"\n - \"Scale Bar tool icon\": creates a scaled and calibra

ted image once a microscope profile has been";


5/22

about= about+"\n choosen from the \"Available Microscope Profiles\" toolbar menu icon.";

about= about+"\n - \"Extract and Edit\" Image tool icon: creates an image with original name from a scaled image";

about= about+"\n without margin and metadata.";about= about+"\n - \"Available Microscope Profiles\" tool bar menu icon:

choice of the appropriate microscope profile";

about= about+"\n to use, before drawing a scale bar.";about= about+"\n - \"Microscope Profiles Manager\" tool bar menu icon co

ntains every functions required to create or";about= about+"\n modify the microscope profiles. It also contains some f

unctions to read the \"Label\" and \"Info\"";about= about+"\n metadata set to the scaled image (see online documentat

ion for more details).";about= about+"\n - \"Online Documentation and Demo\" tool bar menu gives

some internet ressources\; documentation,";about= about+"\n scaled and unscaled images samples and a demo set of mi

croscope profiles for training.";about= about+"\n - Click on the \"Version and Update Infos\" ImageJ tool

bar icon to look for new versions.";about=about + "\n---------------------------------------------------------------------------------";

about=about +"\nAuthor : Gilles Carpentier"+"\nFaculte des Sciences et Technologies"+"\nUniversite Paris 12 Val de Marne, France.";

about=about + "\n---------------------------------------------------------------------------------\n";

about=about +"\nThis tool is inspired from the scalling functionalitiesof the \"3FluoLablelingExploringTools\" available ";

about=about +"\non the ImageJ web site: http://rsb.info.nih.gov/ij/macros/tools/3FluoLablelingExploringTools.txt";

about=about + "\n---------------------------------------------------------------------------------\n";

about=about+ testGetArrayFromProfile();showMessage(about);// from PrintToTextWindow macro available at the http://rsbweb.nih.gov/i

j/macros/PrintToTextWindow.txt// author: Wayne Rasbandtitle1 = "Infos for the \"Scale Bar Tools for Microscopes\"";title2 = "["+title1+"]";f = title2;if (isOpen(title1)) {

print(f, "\\Update:"); // clears the windowprint(f, about);

selectWindow (title1);} else {run("New... ", "name="+title2+" type=[Text File] width=80 height

=16");print(f, about);

}}

macro "Version and Update Infos Action Tool - CcccD5fD6fD7fD8fD9fC78bD17D19D2aD33D37D3bD42D4cD75D95DceDd5Dd9De6Df7Df9CddeDa3C36bD27D28D3aD57D58D59D66D76D77D86D87Da7Db8Dd6De8De9CeeeD00D01D02D04D06D07D08D09D0bD0dD0fD10D11D12D14D1bD1dD1fD20D21D22D2dD30D31D32D40D46D47D48D49D50D5bD60D70D71D72D74D7dD80D81D82D84D8dD90D91D92D94D9dDa0Da1Da2Da4Db0Db1DbbDc0Dc1Dc6Dc7Dc8Dc9Dd0Dd1Dd2De0De1De2DedDf0Df1Df2Df4DfbD

fdDffC8beD3cD3dD4dD5aD6aD79D7aD7bD85D8bD9aDaaDc3Dc4Dd3Dd4CeeeD03D05D0aD0cD0eD13D15D1cD1eD23D2eD3eD4aD55D6cD73D7cD7eD83D8cD8eD93D9cD9eDb5DcaDdeDe3DeeDf3Df5DfcDfeC559D18D26D34D35D36D41D51D61DafDbfDcfDdaDdbDddDeaDf8CcddD2fD5cD6dD6eDabDb2Db4Dc2


6/22

DefC99bD16D24D39D45D54D56D64D65Da5DacDb6DbcDcbDd7DecDfaCdefD67D8aC59dD29D2bD68D69D78D88D96D97D98D99Da6Da8Da9Db9De5De7CacdD1aD2cD38D4bD4eD5dD5eD6bD89D9bDb3DbaDc5Dd8De4Df6C348D25D43D44Db7DccDdcDebCcccD3fD4fDdf" {

VersionInfos ();}

function setScaleBarre () {

requires("1.42n");// check for a previous calibration by this toolmetalabel=getMetadata("Label");metainfo=getMetadata("Info");if (metalabel != "" && (indexOf(metainfo, "") >=0)) exit ("This

image has already been scaled\:\n"+metalabel);if (microscope1[0] == "") exit ("First select a microscope profile from

the blue microscope menu");var calibdata = microscope1;setBatchMode(true);imageid=getImageID();depth = bitDepth; nbslice = getSliceNumber();

objectlist = getlistobj (calibdata);if (otherobjecvalue != 0){objectlist[6] = otherobjective;

} else {model=objectdata[0];

}reponseUser=0;while (reponseUser==0) {resultchoices=userparameters (imageid);}if (pixobj==6) {

resultchoices[7]=otherobjective;objectlist[6]=otherobjective;

} else {model=objectdata[0];

}//blackmarge =(hightcom*nblinecom);//hightnblinecom : hight of a line of info//nbline : nb of line of info//hightcom : hight of the scaleif (scaleset == 1 scalebarset ==1) {blackmarge =(hightnblinecom* (nbl

inecom * infoset) + hightcom); noscaleLine = 0;}if (scaleset == 0 && scalebarset ==0) {blackmarge =(hightnblinecom* (nbl

inecom * infoset)); noscaleLine = 1;}makeBottomMargin (imageid);selectImage (imageCalibid);run("Set Scale...", resultchoices[9]);

SetBar (imageCalibid,resultchoices[7],resultchoices[10],-1,imagex,imagey);if (autosave == 1) AutoSaveCalib (imageid,imageCalibid);setBatchMode("exit and display");

}

function extractAndEditImage () {initScaled=getImageID();xsc = getWidth(); ysc = getHeight();namesc= getTitle;setBatchMode(true);metalabel=getMetadata("Label");metainfo=getMetadata("Info");

pref= ""; suff ="";if (metalabel == "" && (indexOf(metainfo, "") < 0)) {exit ("This

image has not been treated by this tool");}


7/22

if (indexOf(metainfo,pref) >0 && indexOf(metainfo,suff) >0) {blackmargeValue = parseFloat (substring (metainfo, (indexOf(metainfo, pr

ef)+lengthOf(pref)), indexOf(metainfo, suff)));} else {exit ("The metadata seems to be corrupted");}pref = "" ; suff = "";if (indexOf(metainfo,pref) >0 && indexOf(metainfo,suff) >0) {

xsizeValue = parseFloat (substring (metainfo, (indexOf(metainfo, pref)+l

engthOf(pref)), indexOf(metainfo, suff)));} else {exit ("The metadata seems to be corrupted");}pref = "" ; suff = "";if (indexOf(metainfo,pref) >0 && indexOf(metainfo,suff) >0) {

ysizeValue = parseFloat (substring (metainfo, (indexOf(metainfo, pref)+lengthOf(pref)), indexOf(metainfo, suff)));

} else {exit ("The metadata seems to be corrupted");}if ((xsc != xsizeValue) (ysc != (ysizeValue + blackmargeValue))) {exi

t ("The size of the image doesn't correspond to the original");}newName=namesc;if (indexOf(namesc,"-sc") > 0) {newName = substring (namesc, 0, indexOf(

namesc, "-sc")); }

selectImage (initScaled);run("Duplicate...", "title=["+newName+"]");setMetadata("Info", "");if (blackmargeValue > 0) {

makeRectangle(0, 0, xsizeValue, ysizeValue);run("Crop");run("Select None");

}setBatchMode("exit and display");

}

// function removing a microscope profile filefunction rmProfFromProfileCat () {

UpdateProfileList();ok=1;nameofprofiles=InstalledProfiles();choix = catalogMicroPref (nameofprofiles,"remove");ijlocation = getDirectory("startup");filetodelete = ijlocation+ microscopeCollection + File.separator+ choix

;if (File.exists(filetodelete )) showMessageWithCancel ("You will delete

the \""+ choix + "\" microscope profile file\. Continue?");trydelete= File.delete(filetodelete);if (trydelete == 1) {print("\\Clear");print ("The \""+ choix+ "\" micros

cope profile file has been deleted");}else {print("\\Clear");print ("The \""+ choix+ "\" microscope profile fi

le can't be delete for unknown reason");}UpdateProfileList();}

// function editing for modification a microscope profilefunction editMicProfile (kind) {

choice="";toutok=0;ijlocation = getDirectory("startup");if (kind == "edit") {

UpdateProfileList();nameofprofiles=InstalledProfiles();choice = catalogMicroPref (nameofprofiles,"edit-modify");ijlocation = getDirectory("startup");

contentOfProf=GetArrayFromProfile(choice);}if (kind == "new") {contentOfProf=newArray(21);}


8/22

while (toutok == 0) {Dialog.create("Editing of the \""+choice+"\" Microscope profile"

);Dialog.addMessage("Modify the values as explained in the documen

tation. Changing name creates a new profile");Dialog.addString("Microscope profile name", contentOfProf[0],30)

;

Dialog.addString("Objective 1", contentOfProf[1],15);Dialog.addNumber("Distance in pixels", contentOfProf[2], 0, 5, "

pixels");Dialog.addNumber("Known Distance in "+um, contentOfProf[3], 3, 8

, um);Dialog.addNumber("Default bar size in "+um, contentOfProf[4], 3,

8, um);

Dialog.addString("Objective 2", contentOfProf[5],15);Dialog.addNumber("Distance in pixels", contentOfProf[6], 0, 5, "

pixels");

Dialog.addNumber("Known Distance in "+um, contentOfProf[7], 3, 8, um);Dialog.addNumber("Default bar size in "+um, contentOfProf[8], 3,

8, um);

Dialog.addString("Objective 3", contentOfProf[9],15);Dialog.addNumber("Distance in pixels", contentOfProf[10], 0, 5,

"pixels");Dialog.addNumber("Known Distance in "+um, contentOfProf[11], 3,

8, um);Dialog.addNumber("Default bar size in "+um, contentOfProf[12], 3

, 8, um);



8, um);Dialog.addNumber("Default bar size in "+um, contentOfProf[16], 3

, 8, um);



8, um); Dialog.addNumber("Default bar size in "+um, contentOfProf[20], 3, 8, um);

Dialog.show();// ansverscontentOfProf[0] =Dialog.getString();// objective 1contentOfProf[1] =Dialog.getString();contentOfProf[2] =Dialog.getNumber();contentOfProf[3] =Dialog.getNumber();contentOfProf[4] =Dialog.getNumber();// objective 2contentOfProf[5] =Dialog.getString();

contentOfProf[6] =Dialog.getNumber();contentOfProf[7] =Dialog.getNumber();contentOfProf[8] =Dialog.getNumber();


9/22

// objective 3contentOfProf[9] =Dialog.getString();contentOfProf[10] =Dialog.getNumber();contentOfProf[11] =Dialog.getNumber();contentOfProf[12] =Dialog.getNumber();// objective 4contentOfProf[13] =Dialog.getString();

contentOfProf[14] =Dialog.getNumber();contentOfProf[15] =Dialog.getNumber();contentOfProf[16] =Dialog.getNumber();// objective 5contentOfProf[17] =Dialog.getString();contentOfProf[18] =Dialog.getNumber();contentOfProf[19] =Dialog.getNumber();contentOfProf[20] =Dialog.getNumber();for (i=0; i= 0 ){

metainfoimage = substring (metaInfos, (indexOf(metaInfos, pref)+lengthOf(pref)), indexOf(metaInfos, suff));

}return metainfoimage;

}

function getMetaInfosMic () {// extract metainfos from the microscope profilemetaInfos = getMetadata("Info"); metainfomicprofile="";

pref=""; suff ="";if ((indexOf(metaInfos, pref)) >= 0 ) {

metainfomicprofile = substring (metaInfos, (indexOf(metaInfos, p


10/22

ref)+lengthOf(pref)), indexOf(metaInfos, suff));}return metainfomicprofile;

}

function testGetArrayFromProfile() {// from the curent microscope profile name, return a profile info record

ed on the hdif (microscope1[0] != "") {

linesOfProfile = getFileContents (microscope1[0]);profilArray= getArrayFromProfile (linesOfProfile);curentprofileInfo="\n Current Microcope Profile\:\n \n";if (profilArray[0] != 0) curentprofileInfo=curentprofileInfo + p

rofilArray[0] + "\n";for (i=1; i


11/22

if (is("composite")==1) {showMessage ("The scaled image will be 24 bit RGB encoded.");run

("RGB Color"); depth = bitDepth;run("Select All");run("Copy");run("Select None");close ();

} else {run("Select None");run("Duplicate...", "title=dup_"+nomdimage);

depth = bitDepth;if (depth == 16 depth == 32) {showMessage ("The scaled image

will be 8 bit grey encoded.");run("8-bit"); depth = bitDepth;}run("Select None");run("Select All");run("Copy");run("Select Non

e");close ();}if (depth == 24) tipeu="\"RGB Black\"";if (depth == 8) tipeu="\"8-bit Black\"";newImage(nomdimage, tipeu, width, (height+blackmarge), nbslice);makeRectangle(0, 0, width, height);setPasteMode("Copy");run("Paste"); run("Select None");

if (blackmarge !=0 ) {setLineWidth(1);setColor(255,255,255) ;drawLine(0, height,width, height);

}imageCalibid=getImageID();

}

function AutoSaveCalib (init,calib) {selectImage(init);chemin=getDirectory("image");if (chemin != "") {

selectImage(calib);nom=getTitle;

path=chemin+nom; format ="tiff";saveAs (format, path);

}}

// Function creating working arrays from the (calibdata) array contaning the microscope(n) data (n=1).// return calibration data in the global array objectdata

function getlistobj (microdata) {for (i=0;i


12/22

}return objectlist;

}

function getCalib (image) {selectImage(image);getPixelSize(unit, pixelWidth, pixelHeight);

if (unit !=um) {calibration = um+" uncalibrated";} else {calibration = ""+ d2s(pixelWidth,4) +" "+unit+" /pixel";}

textinfo="Current spatial calibration is ("+calibration+" )" ;return textinfo;

}

function userparameters (image) {// Current calibration (pixel are supposed to be squared) :if (model == "") {model=objectdata[0];}textcalib=getCalib (image);if ( model != "" && model != objectdata[0]) {diaMicro="Other for Microsc

ope Model: "+ model;} else {diaMicro="Calibrating for Microscope Model: "+ model

;} Dialog.create("User settings for the image acquisition.");Dialog.addMessage (diaMicro);Dialog.addChoice(textcalib, objective,obj);Dialog.addCheckbox("Draw a scale bar", scalebarset);Dialog.addCheckbox("Write scale", scaleset);Dialog.addCheckbox("Write infos", infoset);Dialog.addCheckbox("Auto-Save the scaled image", autosave);Dialog.show();obj = Dialog.getChoice();scalebarset = Dialog.getCheckbox();scaleset = Dialog.getCheckbox();infoset = Dialog.getCheckbox();

autosave = Dialog.getCheckbox();userchoices[7] = obj;defaultbar=""; pixdist=""; scaleunit=""; knowndist=""; spcalibration="";if (obj == objectlist[1]) {

pixdist= objectdata[1]; knowndist=objectdata[2];scaleunit=um;defaultbar=objectdata[3]; pixobj=1;

}if (obj == objectlist[2]) {



pixdist= objectdata[7]; knowndist=objectdata[8];scaleunit=um;defaultbar=objectdata[9]; pixobj=3;}if (obj == objectlist[4]) {




}if (obj == "Uncalibrated") {

pixdist= 0; knowndist=0;scaleunit="pixel";defaultbar=100;pixobj=

0;}if (obj == "Unchanged" ) {


13/22

pixdist= 100; knowndist=(pixelWidth*100);scaleunit=unit;defaultbar=50;pixobj=0;

}if (obj == "Other") {

other (image);}if (unit !=um && obj == "Unchanged") userchoices[8] = 0;

if (pixobj > 0 && pixobj< 6) model = objectdata[0];spcalibration= "distance="+pixdist+" known="+knowndist+" pixel=1 unit="+

scaleunit;userchoices[9] =spcalibration;userchoices[10]=defaultbar;getPixelSize(unit, pixelWidth, pixelHeight);if (obj== "Uncalibrated") {

objectcode= 0;userchoices[8] = 0;

}if (obj != "no choice") reponseUser =1;if (obj == "-") {obj="no choice"; userchoices[7]="no choice";reponseUser

=0;} return userchoices;}

/////////////////////////////////////////////////////////////////////////////////////////////////// Function for spacial calibration with other data than these contained in themicroscope specific array./////////////////////////////////////////////////////////////////////////////////////////////////

function other (image) {if (objectdata[0] == model) model ="";

textcalib=getCalib (image);if (otherpixdist


14/22

///////////// Function drawing a scale bar in the lower black margin.////////////////////////////////////////////////////////////////////////////////////////////

function SetBar (targetid,objec,baresize,spacer,imagex,imagey) {metaLabelMicro="";

metaInfoMicro="";single=0;if (spacer == -1) single=1;selectImage (targetid);largimage = getWidth();hautimage =getHeight();getPixelSize(unit, pixelWidth, pixelHeight);pixbar= floor(baresize/pixelWidth);if (pixbar >= (largimage/5)) {

while (pixbar >= (largimage/5)) {pixbar= floor(baresize/pixelWidth);

baresize = floor(baresize / 2);

}}if (single==0) maxcustbar= floor((pixelWidth*(largimage + 3*spacer))/4);if (single==1) maxcustbar= floor((pixelWidth*largimage )/4);if (maxcustbar == 0) maxcustbar =1;custuserbar = 0;if (scalebarset == 1) {

while (custuserbar < 1 custuserbar > maxcustbar){if (baresize == 0) baresize =1;message="Advised size of the bar, for "+objec+" : " + ba

resize + " "+unit+". You can set a custom size to from 1 to "+ maxcustbar + " "+unit+ " - Current value =";

if (lastCustuserbar != 0 && lastCustuserbar 150) {

xobjec=((baresize/pixelWidth) + 20); yobjec=(imagey + hightnblinecom +hightnblinecom/2);

if (scalebarset == 0) xobjec=10;setColor(0, 255, 0);setFont("SansSerif", 12,"bold");

if (scaleset == 1) {drawString(thescale, xobjec, yobjec);}}if (infoset == 1) {


15/22

// Insert objective in the black margin (line 1).setColor(0, 255, 255);if ((largimage+130) > 50) {

xobjec=10; yobjec=(imagey + (blackmarge/nblinecom + hightnblinecom *(1-noscaleLine)));

drawString(objec, xobjec, yobjec);}

if (pixobj==6){// Insert zoom and additional info in the black margin (

line 1).setColor(0, 255, 255);message="Zoom factor (lsm): "+zoom;if (largimage > 290) {

xobjec=70; yobjec=(imagey + (blackmarge/nblinecom + hightnblinecom *(1-noscaleLine)));

drawString(message, xobjec, yobjec);}

}// Insert the date in the black margin (line 2).

thedate = GetTime ();setColor(150, 150, 255);if (largimage > 290) {

xobjec=10; yobjec=(imagey + (blackmarge/nblinecom +(2-noscaleLine)*hightnblinecom ));

drawString(TimeString, xobjec, yobjec);}// Insert the model of microscope corresponding to the scaling v

alues in the black margin (line 3).setColor(150, 150, 255);message="Microscope model: "+model;if (largimage > 290) {

xobjec=10; yobjec=(imagey + (blackmarge/nblinecom +(3-no

scaleLine)*hightnblinecom ));drawString(message, xobjec, yobjec);

}}if (metaset == 1) {

// compile meta label:metaLabelMicro= metaLabelMicro + model + " \; " + objec + " \; "

;if (pixobj==6){metaLabelMicro = metaLabelMicro + "Zoom: "+zoom +

" \; ";}metaLabelMicro = metaLabelMicro + thescale +" ";setMetadata("Label", metaLabelMicro);

// compile meta infos for current imagemetaInfoMicro=metaInfoMicro + "";metaInfoMicro=metaInfoMicro + "" +model+ "";metaInfoMicro=metaInfoMicro + "" +objec + "";metaInfoMicro=metaInfoMicro + "" +zoom + "";metaInfoMicro=metaInfoMicro + "" +d2s (pixelWidth, 3) + "

";metaInfoMicro=metaInfoMicro + "" + unit + "";metaInfoMicro=metaInfoMicro + "" + baresize + "";metaInfoMicro=metaInfoMicro + "" + blackmarge + "";metaInfoMicro=metaInfoMicro + "" + imagex + "";metaInfoMicro=metaInfoMicro + "" + imagey + "";

metaInfoMicro=metaInfoMicro + "";// compile meta infos for the current image microscope profilemetaInfoMicro=metaInfoMicro +"";


16/22

for (i=0; i 0 && listerm[0] != "No microscope profile found") {

Dialog.create("List of Microscope Profiles");message="Choose the microscope profile to "+ action;Dialog.addChoice(message, listerm);Dialog.show();chosenProfile = Dialog.getChoice();return chosenProfile;

} else {exit ("No microscope profile found");}}

// Function giving the number (NumberOfProfiles) of profiles contained a file li

st (lprofile).function getProfileNumber (lprofile) {

NumberOfProfiles=0;


17/22

for (i=0; i lengthOf("-MicProf.txt")) NumberOfProfiles ++;

}return NumberOfProfiles;

}

// Function giving a text profile from a profile arrayfunction getProfileFromArray (arrayToTreat) {

pref=""; suff ="";textFomArray=newArray (2); // 0 contains the title of the array, 1 conta

ins the profile text itselftextFomArray[0]=arrayToTreat[0]; text="";for (i=1; i


18/22

listoffiles=getFileList(microlocationFolder);NumberOfProfiles=getProfileNumber (listoffiles);if (NumberOfProfiles !=0) {

var catalogue= newArray (NumberOfProfiles);var shortCat= newArray (NumberOfProfiles);nbProf=0;for (i=0; i lengthOf("-MicProf.txt")) {catalogue [nbProf]=listoffiles[i];shortCat [nbProf]=replace(catalogue [nbProf], "-

MicProf.txt", "");nbProf++;

}}

} else {var catalogue= newArray ("No microscope profile found");var shortCat= newArray ("No microscope profile found");

}if (editMode ==0) return shortCat;if (editMode ==1) return catalogue;

}

function instalDemoCollection () {microscope1 = newArray("Axiovert 10 CCD Axiocam MRm","Obj 5x achro","772

","1000","100","Obj 5x neofluo","759","1000","100","Obj 10x achro","755","500","50","Obj 10x neofluo","763","500","50","Obj 20x achro","612","200","25");

demoProfil=getProfileFromArray (microscope1);saveMicroPref (demoProfil[0],demoProfil[1]);microscope1 = newArray("Olympus BH-2 CCD Scion","Obj 4x","832","1000","1

00","Obj 10x","207","100","50","Obj 20x","417","100","50","Obj 40x","833","100","10","Obj 100x","185","9","10");

demoProfil=getProfileFromArray (microscope1);saveMicroPref (demoProfil[0],demoProfil[1]);microscope1 = newArray("Leica Palermo","Obj 10x","658","500","50", "Obj

20x","525","200","50","Obj 40x","530","100","10", "Obj 63x","827","100","10", "Obj 100x","1312","100","10");

demoProfil=getProfileFromArray (microscope1);saveMicroPref (demoProfil[0],demoProfil[1]);microscope1 = newArray("Leitz Aristoplan CCD CoolSnap ","Obj 6,3x","436"

,"500","100","Obj 10x plan","549","400","50","Obj 25x Fluotar","1035","300","50","Obj 40x Fluotar","1103","200","10","Obj 100x oil Fluotar","1103","80","10");

demoProfil=getProfileFromArray (microscope1);saveMicroPref (demoProfil[0],demoProfil[1]);microscope1 = newArray("Nikon TE2000 Salpetriere CCD Hamamatsu","Obj 10x

ph1","1160","500","50", "Obj 20x plan fluo","928","200","50","-","1","1","1", "-","1","1","1","-","1","1","1");

demoProfil=getProfileFromArray (microscope1);saveMicroPref (demoProfil[0],demoProfil[1]);UpdateProfileList();

}

function UpdateProfileList() {// update the profile listkind="toolsets";macroname="Scale Bar Tools for Microscopes.txt";

macropath=getDirectory("macros") + kind + File.separator+ macroname;if (!File.exists(macropath)) {exit ("Record this tool into the \"ImageJ\

/macros\/toolset\" repertory folder\nwith the name \"" +macroname+ "\", to use i


19/22

t.");}run("Install...", "install=["+macropath+"]");

}

function netTest () {erNetMessage ="Error: ";testlink = "http://rsb.info.nih.gov/ij/macros/Arrays.txt";

if (indexOf (File.openUrlAsString(urllist), errorNetMessage) >0) exit("You need an internet access to run this function.");}

function OpenImageLink(link,name,question) {// Check if already downloaded.demoimalocation = getDirectory("startup");fildestination = demoimalocation+ "Downloaded Demo Images/" + name;if (File.exists(fildestination)) {

if (question ==1 ) showMessageWithCancel ("The \"" + name + "\"has already been downloaded. Open it?");

open(fildestination);

}else {netTest ();showMessageWithCancel ("ImageJ will download a demo image. Conti

nue?");run("URL...", "url=["+link+"]");imageid = getImageID();nomdimage = getTitle;// Create a repertory in ImageJ folder.ImaDemo = demoimalocation+"Downloaded Demo Images"+File.separato

r;File.makeDirectory(ImaDemo);if (!File.exists(ImaDemo)) exit("Unable to create directory, som

ething wrong in the ImageJ folder");selectWindow(nomdimage);save(""+ImaDemo+""+ nomdimage +"");

}}

function doc () {netTest ();showMessageWithCancel ("A notice is avaible on line. Open it with your

default web browser?");run("URL...", "url=["+onlinedoclink +"]");

}

// -------------------*** Additionnal code for on line update resources ***-----------------------------

//Developer info//Kind:Toolset//Title:"Scale Bar Tools for Microscopes"//Version:1.0//Date: 11/05/2009//Origin:NIH//End info

function VersionInfos () {// variables for on line update resourcesbeginsign="//Developer info";endsign="//End info";


20/22

kind="toolsets/";urlrep="http://image.bio.methods.free.fr/ij/ijmacro/scalebar/";name="Scale Bar Tools for Microscopes.txt";namedev="Scale Bar Tools for Microscopes-dev.txt";favoritefoldername= "Image.Bio.Methods";version=versionMessage();if (indexOf(version, "install it?" ) > 0 ) {

macrotext=getdistantmacro (namedev,urlrep);macrolocal="";macropath=getDirectory("macros")+kind+namedev;if (File.exists(macropath)) {macrolocal=File.openAsString(macrop

ath);}if (macrotext != macrolocal) {

//perfom the installationDialog.create("New version installation option");Dialog.addMessage(version);Dialog.addCheckbox("Install a Plugin Shortcut?", 0);Dialog.addMessage("(This option provides a shortcut in t

he plugins menu of ImageJ, making easier\nthe next use of the new installed version).");

Dialog.show();plugin= Dialog.getCheckbox();f= File.open(macropath);print (f,macrotext);File.close(f);if (plugin ==1) {InstallPluginsStarter(namedev);}message="The installation of the "+giveDevInfo (macrotex

t,1)+ " "+ giveDevInfo (macrotext,2)+ "is completed.";message=message+ " Do you want to run it?";showMessageWithCancel(message);run("Install...", "install=["+macropath+"]");

}} else {showMessage (version); // comment without installation available

}}

function versionMessage() {version="";if (getDirectory("startup") == 0) exit ("Unable to find the startup dire

ctory, something wrong in the ImageJ folder");if (getDirectory("macros") == 0) exit ("Unable to find the macros direct

ory, something wrong in the ImageJ folder");MacroPath=getDirectory("macros");thismacropath=MacroPath+kind+name;if (! File.exists(thismacropath)) exit ("This macro has to be recorded u

nder the name of \"" +name+"\"\ninto the \"macros/"+kind+"\" folder of ImageJ.")

; macrotext=File.openAsString(thismacropath);macrotextdistant=getdistantmacro (namedev,urlrep);version="";macrolocal="";version=version + "\n \nThis version of the " + giveDevInfo (macrotext,1

) + " " + giveDevInfo (macrotext,2);version=version + "is provided by the " + giveDevInfo (macrotext,5)+ " w

eb site.";version=version + "\nVersion number: " + giveDevInfo (macrotext,3)+ " -

" + giveDevInfo (macrotext,4) +".";if (macrotextdistant !="" ) {

new=giveDevInfo (macrotextdistant,3);old=giveDevInfo (macrotext,3);

if (new > old) {macropath=getDirectory("macros")+kind+namedev;if (File.exists(macropath)) {macrolocal=File.openAsStrin


21/22

g(macropath);}if (macrotextdistant != macrolocal) {

update="\n \nA new version "+new+ " is availableon the " +giveDevInfo (macrotextdistant,5)+ " web site: ";

update=update+ "\n \nDo you want to install it?";

} else {

update ="\n \nThe latest "+new+" version called\"" +namedev+ "\" provided by \nthe "+giveDevInfo (macrotextdistant,5) +" web site has already be installed";

update = update+ " in the \"" +kind+ "\" repertory \nof ImageJ.";

}} else {

update="No new version available.";}version=version +"\n" + update ;

}return version;

}function giveDevInfo (text,n) {

lines=split(text,"\n");if ( (indexOf(text, beginsign) -1) {distantmacrolink=substring(distantmacrolink, 0,(indexOf(distantmacrolink, " ")))+"%20"+substring(distantmacrolink, (indexOf(distantmacrolink, " ")+1),lengthOf(distantmacrolink) );

}}showStatus("Internet link...");macrotextnih =File.openUrlAsString(distantmacrolink);showStatus("");

} else { showMessage ("No internet connection to looks for new version.");}

return macrotextnih;}

function InstallPluginsStarter(macroname) {// from MacroPluginShortcutsTool.txt


22/22

codestarter = "run\(\"Install...\", \"install=[\"+getDirectory(\"macros\")+\""+kind+ macroname + "\]\"\);";

if (getDirectory("plugins") == "") exit ("Unable to find the Plugins directory; something wrong in the ImageJ folder.");

if (endsWith(macroname, ".txt") endsWith(macroname, ".ijm")) pluginname = substring(macroname, 0, (lengthOf(macroname)-4));

StarterDir = getDirectory("plugins")+favoritefoldername+File.separator;

File.makeDirectory(StarterDir);if (!File.exists(StarterDir)) exit ("Unable to create "+favoritefolderna

me+" Macros directory, something wrong in the ImageJ folder.");starterplugin = StarterDir + pluginname +"_ .ijm";f= File.open(StarterDir + pluginname +"_ .ijm");print (f,codestarter);File.close(f);showMessage ("The plugin shortcut \"" +pluginname+ "\" will be available

after\nImageJ restarting, in the \"Plugins->" + favoritefoldername + "\" menu.");}

// *** End of additionnal code for on line update ressources ***

scale bar tools for microscopes

Documents