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Non-destructive Marking with ObjectJ: Practical Examples. Norbert O.E. Vischer Stelian Nastase. University of Amsterdam. History. W. Rasband. NIH Image. ImageJ. 1990. 1995. 2000. 2005. 2008. Non-destructive marking:. Object-Image. ObjectJ. N. Vischer. + S.Nastase. Project #1
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Non-destructive Marking with ObjectJ: Practical Examples Norbert O.E. Vischer Stelian Nastase University of Amsterdam
History W. Rasband NIH Image ImageJ 1990 1995 2000 2005 2008 Non-destructive marking: Object-Image ObjectJ N. Vischer + S.Nastase
Project #1 Multi-parameter measurements of bacterial cells shown in hyperstacks
Escherichia coli 1 µm Phase contrast Fluor. CFP DNA Fluor. YFP origin terminus
Desired output: axis length mean diameter constriction relative spot positions
13 Composite object keeps cell parameters together
ObjectJ provides 3 more windows: Project Window ObjectJ Tools ObjectJ Results … for setting up a project
Create Kill Move Select Convert to ROI User-defined palette of item types
Continuous vector layer Discrete pixels
File operations Housekeeping Special ObjectJ Windows Project Macros
Analysis of fish eggs using ObjectJ Anne-Christine Knag and Anders Thorsen, Norway Atlantic cod, Gadus Morhua
1 mm Eggs of Atlantic Cod
diameter = ? centre = ? d = 148
Conclusions: what we found useful: • clean desktop • easy to detect bugs and artifacts • slide show • discussing results with others artifact what people find difficult: • what you see is saved in two different files • understanding composite objects • macro programming what to improve bug • stability • efficiency (large number of objects) • documentation and website
ObjectJ Developed with NetBeans Open Source Still Beta http://simon.bio.uva.nl/objectj
Credits: Amsterdam: StelianNastase Conrad Woldringh Tanneke den Blaauwen DorusGadella Bergen: Anders Thorsen Anne-Christine Knag Elsewhere: WayneRasband Tudor organizers ImageJ community