Fiji Is Just ImageJ an open source platform for biological image analysis
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1 Fiji Is Just ImageJ an open source platform for biological image analysis Pavel Tomancak Max Planck Institute of Molecular Cell Biology and Genetics in Dresden (MPI-CBG) OME meeting, Paris June 15th
2 Why Open Source? if you can t see the code of a piece of commercial software, then you cannot say what the software really does, and this is not scientific. Andrew C. Oates
3 Why Open Source? Biological image analysis problems are complex and require novel application of state-ofthe-art computer vision algorithms 4d SPIM recording of Drosophila embryogenesis
4
5
6 What is Fiji?
7 What is Fiji? Fiji Is Just ImageJ
8 What is Fiji? Fiji Is Just ImageJ Linux Ubuntu ImageJ Fiji
9 What is Fiji? Fiji Is Just ImageJ Linux Ubuntu ImageJ Fiji ba#eries included, some assembly required
10 Why Fiji?
11 Why Fiji?
12 Registration Confocal imaging in tiling mode SPIM multi-view registration Preibisch et al. Bioinformatics 2009 Preibisch, Saalfeld et al. Nature Methods 2010 serial section Transmission Electron Microscopy Saalfeld et al. Bioinformatics 2010
13 Registration Confocal imaging in tiling mode SPIM multi-view registration Preibisch et al. Bioinformatics 2009 Preibisch, Saalfeld et al. Nature Methods 2010 serial section Transmission Electron Microscopy Saalfeld et al. Bioinformatics 2010
14 33,000 images
15 Many other Fiji projects TrakEM2 3D Viewer Feature Extraction Stitching 2D/3D bunwarpj Simple Neurite Tracer
16 Who should use Fiji? Biologists Bioinformaticians Software developers Computer Vision Researchers
17 Batteries included Normal biologist users Coherent menu structure Tutorials and documentation
18 Biology hackers Scripting languages Scripting interpreter
19 Software developers Version control Build system Java libraries Communication channels (IRC, mailing list, wiki) strict Open Source
20 Software developers Version control Build system Java libraries Communication channels (IRC, mailing list, wiki) strict Open Source
21 Computer vision professionals imglib dimension, type and storage independent image library Stephan Preibisch Stephan Saalfeld
22 Computer vision professionals imglib dimension, type and storage independent image library Stephan Preibisch Stephan Saalfeld
23 Computer vision professionals imglib dimension, type and storage independent image library Stephan Preibisch Stephan Saalfeld
24 Everybody
25 The birth of Fiji plugin 1. Download the source code from git repository
26 The birth of Fiji plugin 1. Download the source code from git repository 2. Write your amazing plugin
27 The birth of Fiji plugin 1. Download the source code from git repository 2. Write your amazing plugin 3. Test it with the Fiji build system on your computer
28 The birth of Fiji plugin 1. Download the source code from git repository 2. Write your amazing plugin 3. Test it with the Fiji build system on your computer 4. Upload it to the repository in Dresden (special branch)
29 The birth of Fiji plugin 1. Download the source code from git repository 2. Write your amazing plugin 3. Test it with the Fiji build system on your computer 4. Upload it to the repository in Dresden (special branch) 5. Wait till Fiji developers say they like it (how long? depends how good the plugin is)
30 The birth of Fiji plugin 1. Download the source code from git repository 2. Write your amazing plugin 3. Test it with the Fiji build system on your computer 4. Upload it to the repository in Dresden (special branch) 5. Wait till Fiji developers say they like it (how long? depends how good the plugin is) 6. If its good, include it into the update system
31 The birth of Fiji plugin 1. Download the source code from git repository 2. Write your amazing plugin 3. Test it with the Fiji build system on your computer 4. Upload it to the repository in Dresden (special branch) 5. Wait till Fiji developers say they like it (how long? depends how good the plugin is) 6. If its good, include it into the update system 7. Next time anybody updates Fiji they will get your plugin
32 Hackathons Two weeks coding sprees where Fiji developers meet and work collaboratively on the Fiji code. Janelia Farm Research Campus 2007,2008 Max Planck Institute in Dresden (MPI-CBG) 2009 European Molecular Biology Laboratory (EMBL) 2010
33 Fiji development visualization
34 Fiji development visualization Dresden Hackathon
35 Fiji development visualization
36 Philosophy Biology Microscopy Bioinformatics Bioimage analysis Software engineering Computer Vision
37 Philosophy Biology Microscopy Bioinformatics Bioimage analysis Software engineering Computer Vision
38 Future of Fiji git imglib plugin architecture updater Johannes Schindelin ImageJ2 ImageJ
39 Future of Fiji git imglib plugin architecture updater Johannes Schindelin ImageJ2 ImageJ
40 Founding Father of Albert Cardona ETH Zurich/ Janelia Farm neurobiologist TrakEM2 Java hacker
41 Founding Mother of Johannes Schindelin MPI-CBG image processing facility leader mathematician git ImageJA passionate pun maker
42 Acknowledgements Fiji developers Stephan Preibisch, Stephan Saalfeld, Benjamin Schmid, Dan White, Jean-Yves Tinevez, Erwin Frise, Gabriel Landini, Verena Kaynig, Greg Gefferis, Ignatio Arganda-Carreras, Mark Longhair, Jan Eglinger, Curtis Rueden and many more Ivan Baines
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