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Practical Applications of Non-Destructive Marking with ObjectJ for Image Analysis

This document provides practical examples of non-destructive marking using ObjectJ, a tool developed for analyzing and marking images in various scientific contexts. It showcases multi-parameter measurements of bacterial cells like Escherichia coli and analyses of fish eggs, particularly Atlantic cod. The content elaborates on creating, managing, and displaying objects within hyperstacks while addressing challenges encountered, such as detecting bugs, artifacts, and enhancing program stability. Contributions from several researchers highlight the importance of collaboration in advancing image analysis tools for biological research.

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Practical Applications of Non-Destructive Marking with ObjectJ for Image Analysis

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  1. Non-destructive Marking with ObjectJ: Practical Examples Norbert O.E. Vischer Stelian Nastase University of Amsterdam

  2. History W. Rasband NIH Image ImageJ 1990 1995 2000 2005 2008 Non-destructive marking: Object-Image ObjectJ N. Vischer + S.Nastase

  3. Project #1 Multi-parameter measurements of bacterial cells shown in hyperstacks

  4. Escherichia coli 1 µm Phase contrast Fluor. CFP DNA Fluor. YFP origin terminus

  5. Desired output: axis length mean diameter constriction relative spot positions

  6. 13 Composite object keeps cell parameters together

  7. Object Visibility in Hyperstacks

  8. Link

  9. ObjectJ provides 3 more windows: Project Window ObjectJ Tools ObjectJ Results … for setting up a project

  10. Project Window: Defining Objects

  11. Create Kill Move Select Convert to ROI User-defined palette of item types

  12. Project Window: Linking Images Drag

  13. Discrete pixels

  14. Continuous vector layer Discrete pixels

  15. File operations Housekeeping Special ObjectJ Windows Project Macros

  16. Demo

  17. Analysis of fish eggs using ObjectJ Anne-Christine Knag and Anders Thorsen, Norway Atlantic cod, Gadus Morhua

  18. 1 mm Eggs of Atlantic Cod

  19. diameter = ? centre = ? d = 148

  20. 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

  21. ObjectJ Developed with NetBeans Open Source Still Beta http://simon.bio.uva.nl/objectj

  22. Credits: Amsterdam: StelianNastase Conrad Woldringh Tanneke den Blaauwen DorusGadella Bergen: Anders Thorsen Anne-Christine Knag Elsewhere: WayneRasband Tudor organizers ImageJ community

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