Non-destructive Marking with ObjectJ:

Practical Examples

Norbert O.E. VischerStelian Nastase

University of Amsterdam

History

Object-Image ObjectJ

+ S.NastaseN. Vischer

Non-destructive marking:

1995

W. Rasband

2000 2005 20081990

NIH Image ImageJ

Project #1

Multi-parameter measurementsof bacterial cells

shown in hyperstacks

Phase contrast

1 µm

Escherichia coli

DNA

terminusoriginFluor. YFP

Fluor. CFP

Desired output:

axis length

mean diameter

constriction

relative spot positions

Composite object keeps

cell parameters together

13

Object Visibility in Hyperstacks

Link

… for setting up a project

ObjectJ provides 3 more windows:

Project Window

ObjectJ Tools

ObjectJ Results

Project Window: Defining Objects

SelectMoveConvert to ROI

KillCreate

User-definedpalette of

item types

Project Window: Linking Images

Drag

Discrete pixels

Discrete pixels

Continuous vector layer

File operations

Housekeeping

Special ObjectJ Windows

Project Macros

Demo

Analysis of fish eggs using ObjectJAnne-Christine Knag and Anders Thorsen, Norway

Atlantic cod, Gadus Morhua

1 mmEggs of Atlantic Cod

diameter = ?centre = ?

d = 148

• clean desktop• easy to detect bugs and artifacts• slide show• discussing results with others

• what you see is saved in two different files• understanding composite objects• macro programming

• stability• efficiency (large number of objects)• documentation and website

what we found useful:

what people find difficult:

what to improve

Conclusions:

bug

artifact

ObjectJ

Developed with NetBeansOpen SourceStill Betahttp://simon.bio.uva.nl/objectj

Credits:

Amsterdam:Stelian NastaseConrad WoldringhTanneke den BlaauwenDorus Gadella

Bergen:Anders ThorsenAnne-Christine Knag

Elsewhere:Wayne RasbandTudor organizers ImageJ community