2018-12-06 - I2K 2018 Dresden Hackathon
From Monday, December 3, 2018 through Friday, December 7, 2018, the Max Planck Institute of Molecular Cell Biology and Genetics hosts ~10 developers at the Center for Systems Biology in Dresden, Germany for a hackathon to develop KNIME Image Processing and ImageJ2/Fiji core infrastructure and plugins.
Gitter channel: https://gitter.im/juglab/Hack1812
- 1 Topics / Technical Discussions
- 1.1 TensorFlow (Debo, Curtis, Benny)
- 1.2 SCIFIO (Gabriel, Curtis)
- 1.3 Governance
- 1.4 Wiki
- 1.5 Servers (Gaby, Debo, Curtis)
- 1.6 Labkit as Labeling Editor for KNIME Image Processing
- 1.7 Simple ImageJ API
- 1.8 Big Data Server
- 1.9 Octtree Like, Compressed, Fast, Bitmaps for Imglib2
- 1.10 HTTPS (Debo, Curtis, Gaby, Tobi)
- 1.11 Updater/Launcher (Debo, Curtis)
- 1.12 Plot Service (Matthias, Curtis)
- 1.13 Curtis
- 1.14 Other
Topics / Technical Discussions
TensorFlow (Debo, Curtis, Benny)
- Plan for TensorFlow: ship native libs both CPU and GPU in lib/<platform> directly;
- TensorFlow update sites and reconcile to new TF version -- add tests
SCIFIO (Gabriel, Curtis)
- Create samples.scif.io, migrate LOCI samples, update scif.io website with a table of samples
- Update scifio-bf-compat to split the mega-format into one per reader/writer
- Code of conduct - https://help.github.com/articles/adding-a-code-of-conduct-to-your-project/ - http://openrespect.org/ (It's written by the author of The Art of Community)
- Update fiji.sc, imagej.net/Fiji, etc. with revised maintainership info
Google Scholar: citation count badges on wiki pages
- What to do about NanoJ using google analytics -- i.e. should we have usage stats?
- [Action item] Ask Ricardo Henriques about it
- Consider what to write onto code of conduct about what should be allowed
Meet at later point in time—and who is going to do it
- What to do about the two different logos: ImageJ vs. Fiji
- Upstream Java issues -- send something shortly after January 15
- [Action item for Ulrik] Writeup from Ulrik and Stephan S. about JavaFX
- [Action item for Ulrik] Writeup from Tobias about Unsafe
- doi in maven pom
- citation badge on wiki pages
Servers (Gaby, Debo, Curtis)
- Server infrastructure overview with Gaby
rsync mirror to pacific.mpi-cbg.de
Labkit as Labeling Editor for KNIME Image Processing
- Node for editing labels in KNIME based on Labkit was created.
- Work is not entirely finish. We plan to finish this work during the Ostrava Hackathon.
- Labkit was extended, and is now able to handle multiple images.
- A labeling datatype to store labels, and track modifications was developed.
Simple ImageJ API
- Discussion between: Deborah, Robert, Curtis, Matthias
- How can we make the scripting in ImageJ2 easier?
- Setup a table, of scripting examples in IJ1 and IJ2. Improve the IJ2 API where ever it's obviously required.
- Write a SimpleIJ gateway, that provides really simple methods for the most frequent tasks in ImageJ.
- A ImageJ2 script recorder could improve the IJ2 API, as it clearly shows where the API is to verbos.
Big Data Server
- Discussion Tobias, Gabriella and Matthias about a mechanism for secure user authentication in Big Data Server (and ImageJ Server).
- It's needed by biologists, that want to share there data with specific users.
- ImageJ Server would also benefit, if the access to the API could be authenticated in a similar way.
Octtree Like, Compressed, Fast, Bitmaps for Imglib2
- Tobias develops a data structure to store bitmap. For iteration, efficient pixels access and little memory foot print at the same time.
- Such data structures can be used to better express labels in imglib2. Even instance segmentations that consist of millions of labels, can be accessed efficiently if a cell image like cache is used.
HTTPS (Debo, Curtis, Gaby, Tobi)
- HTTPS java-version-check
- move list of update sites to a GitHub repository -- off the wiki
Updater/Launcher (Debo, Curtis)
- Add version to db.xml.gz schema
- Make the updater smart enough to support serving maven artifacts
- Migrate "make fiji package" to imagej updater
- improve "make package" to only zip up non-update-site things ("online mode")
- Eliminate native launcher in favor of javafx + java-launches-java scheme
Plot Service (Matthias, Curtis)
- Get it merged to scijava-common / scijava-ui-swing
- Merge script editor PRs
add "browse javadoc" and "browse source" options for selected code? e.g. on IOService opens DefaultIOService on GitHub or javadoc.scijava.org
- Finish algorithms branch of imagej-mesh -- Move imagej-ops mesh package and algorithms into imagej-mesh -- See WIP commit message on algorithms branch -- Update imagej-ops to call migrated routines
- Remove modern mode from GUI (Debo, Curtis)
- Labkit + KNIME (Matthias, Tim-Oliver, others)
- KNIME+TensorFlow+Server (Tim-Oliver, Benny)
- Ilastik tracking (Carsten, Mangal)
- Scenery + KNIME including BigVolumeViewer (Ulrik, Gabriel)
- Image metadata (Carsten, Marcel)