2017-12-04 - Fiji + KNIP hackathon
From Monday, December 4, 2017 through Friday, December 15, 2017, the Max Planck Institute of Molecular Cell Biology and Genetics hosts ~50 developers at the Center for Systems Biology in Dresden, Germany for a hackathon to develop ImageJ2 and Fiji core infrastructure and plugins.
- 1 Voluntary hackathon calendar
- 2 Hackathon google doc
- 3 Hackathon on Twitter (#hackdd17)
- 4 Technical Discussions
- 5 Hackathon Progress
- 5.1 ilastik - (Dominik Kutra, Carsten Haubold)
- 5.2 SciView - (Kyle Harrington, Ulrik Günther, Curtis Rueden)
- 5.3 ImageJ server - (Curtis Rueden, Petr Bainar)
- 5.4 SciJava - (Curtis Rueden)
- 5.5 ImageJ Ops - (Curtis Rueden)
- 5.6 ImageJ Legacy - (Curtis Rueden)
- 5.7 ImageJ Launcher - (Curtis Rueden)
- 5.8 Bio-Formats - (Curtis Rueden)
- 5.9 ClearControl / ClearVolume / ClearCL (Robert Haase, Loic Royer)
- 5.10 ImgLib2 IJ - (Matthias Arzt)
- 5.11 Labkit - (Matthias Arzt)
- 5.12 ImgLib2 ROIs - (Alison Walter, Tobias Pietzsch, Curtis Rueden)
- 5.13 ImageJ-OMERO - (Alison Walter, Josh Moore)
- 5.14 BigCAT (Philipp Hanslovsky)
- 5.15 scyjava & imglyb (Philipp Hanslovsky, Curtis Rueden)
- 5.16 Image Sequence Registration Plugin (Christian Tischer)
- 5.17 Mastodon (Jean-Yves Tinevez, Tobias Pietzsch)
- 5.18 TrackMate & MaMuT (Ulrik Günther, Kyle Harrington, Jean-Yves Tinevez)
Voluntary hackathon calendar
Hackathon google doc
Hackathon on Twitter (#hackdd17)
N5, not HDF5
For more info on N5, check out the github repository here.
- feels like HDF5, but stores chunks(blocks) in separate files in the file system.
- is a Java library, but Constantin Pape already wrote a C++/python version of it: z5 (also matches "zarr" library), https://github.com/constantinpape/z5
- attributes are stored in an additional JSON file
- Discussion: should we define standard now as to how data should be stored in there to prevent an emergence of a zoo of different flavors as there is for HDF5?
- how to do time series where each timestep / angle could have different image size
- if we want a general "N5 viewer" for images, we'd have to add calibration data
- put this information around the N5 dataset, because it behaves more like a dataset within an H5 file.
- Perhaps make it versioned? Because a duck is not always a duck...
- why another file format?
- parallel writes (awesome for clusters with shared filesystem)
- there is a special type for label blocks
- blocks can have a halo
- the block grid does not need to be filled dense, some blocks could be missing
- couldn't this just be another flavor of HDF5?
- are parallel writes to the same block prevented by some kind of locks?
- the HDF5 team should be included in the discussions to learn from their mistakes - there is lots of information on parallel writing of HDF5 files out there
- Try to write a N5 dataset into a FUSE filesystem/file??? Could this be a work-around for the many-small-files issue?
- There is a fork of BigDataViewer for JavaFx. 
- BigDataViewer will be splitted into a UI independent part, and the Swing UI. This will make it possible to merge the JavaFx and Swing Version of BigDataViewer .
We discussed opportunities to improvement for the Bdv design:
- Slim the core of bdv, make it less smart and more predictable.
- Bdv handle for different UI toolkits,
- Use property pattern for settings like active source ...
- Actively add/remove views
- Update views (force cache-dropping) - for BDV add/remove views
- Access to color settings, overlap rendering, …
- Allow Grouping of views (externally is ok)
- Consider Accumulator / Composite that works with type other than ARGBType
- Make it easy to disable or replace Dialogs
- Make it easy to remove an overlay
- BdvVistools show function for converters/volatile
Matrix and Vector libraries
- Discussion notes: https://docs.google.com/document/d/12a_9AhFMJywm7y-SfZHuWB5cXwEkpCGt03Sxq8JVfMI/edit
- Compared different matrix and vector libaries: https://github.com/imglib/imglib2-matrix-shootout
- use ojAlgo for N-D matrix operations
- vector3 and vector4 is a complicated conclusion. probably use mastodon and JOML
- initial focus on embarassingly parallel data
- specific parallel (cluster) implementation will be abstracted
- from the system architecture point of view, the design can be inspired by the search bar feature implementation
- started use case definition
ilastik - (Dominik Kutra, Carsten Haubold)
- developed an ImageJ2 plugin that allows to stream raw data and predictions from the work in progress ilastik processing backend: https://github.com/ilastik/org.ilastik.bdvsource
- discussed with Philipp Hanslovsky about the benefits of using the N5 format for communication
- the label block format together with the fact that datasets can be stored sparse could be a great foundation for label storage / communication
- played around with Constantin Pape's C++/Python N5 reader as available format on the ilastik server
- noticed that the only thing needed to serve a N5 dataset on the web is to serve the directory contents. Philipp wrote a N5 REST reader for BigCAT to talk to the ilastik server that way
- worked on some caching problems in the ilastik server
- discussed possible interfaces between Matthias Arzt's LabKit and ilastik-backend for interactive segmentation in ImageJ/BigDataViewer with an ilastik classifier backend
SciView - (Kyle Harrington, Ulrik Günther, Curtis Rueden)
- set up automatic deployment of Fiji update site that works on all operating sustems
- imglib2 images as textures on 3D objects
- imagej2-style logging
- public availability of SciView plugin
ImageJ server - (Curtis Rueden, Petr Bainar)
- discussed its design with respect to the ImageJ/Fiji architecture as well as its future use cases
- identified the most imminent issues, raised them on GitHub and brainstormed possible solutions
- demoed the new client to the community
- encouraged members of the community to use annotations specifying whether a SciJava plugin can run headless or not
SciJava - (Curtis Rueden)
- Added a minimum Java build version feature to pom-scijava-base (scijava/pom-scijava-base@54bf6664).
#@scriptdirective (scijava/scijava-common@d9dce68b, scijava/scijava-common#294).
- In response to a question from Klim Kolyvanov, cleaned up the
PrefServiceand fixed related parameter persistence bugs (scijava/scijava-common@195878b7).
- With Robert Haase and Deborah Schmidt, developed a
SearchServiceAPI for extensible text-based searches (scijava/scijava-search). Initially supports searching SciJava modules (e.g. commands and scripts) and ImageJ web resources. Also offers a code snippet executer, as suggested by Kyle Harrington.
- In response to a question from Richard Domander, fixed a bug with
DynamicCommandvalidater method callbacks (scijava/scijava-common@13e4ec32).
- In response to a question from Richard Domander, added a short-term workaround for the fact that you cannot execute
ImageJ Ops - (Curtis Rueden)
- Merged Gabriel Selzer's improvements to the transform namespace for intervals (imagej/imagej-ops#515).
- Merged Vladimír Ulman's Gabor and bigauss filters (imagej/imagej-ops#485).
- Merged Gabriel Selzer's Frangi vesselness filter (imagej/imagej-ops#525).
- Merged Brian Northan's bug-fix to the IFFT op (imagej/imagej-ops#529).
- Merged Brian Northan's diffraction-based kernel, useful for generating PSFs for deconvolution (imagej/imagej-ops#530).
- Merged Kyle Harrington's morphological thinning ops, ported from KNIME (imagej/imagej-ops#317).
- Merged Eike Heinz's Sobel and Hessian filters (imagej/imagej-ops#349).
- With Gabriel Einsdorf, worked on fusion ops for combining RAIs that overlap (imagej/imagej-ops#230). PR was closed without merge, but a demo of RAI fusion was pushed to my sandbox (ctrueden/sandbox@b5518112).
- In response to a question from Klim Kolyvanov, pushed an example of using the slice op to iterate an op over planes (ctrueden/sandbox@753dd703).
ImageJ Legacy - (Curtis Rueden)
- In response to a question from Klim Kolyvanov, fixed bug with parameter visibility (imagej/imagej-legacy@e89ce40e).
ImageJ Launcher - (Curtis Rueden)
- Merged Stefan Helfrich's CI configuration for AppVeyor and Travis CI (imagej/imagej-launcher#49).
- Made minimal changes required for the the Launcher to work with Java 9 (imagej/imagej-launcher@e501d695).
Bio-Formats - (Curtis Rueden)
- In response to a question from Christian Tischer and David Hörl, filed a PR to enable the high-level Bio-Formats API to accept file patterns directly (openmicroscopy/bioformats#3019).
- Fixed new and existing Java-8 installations of Fiji to work properly with Bio-Formats again (1). This entailed creating a script that instructs users of the old Java 6 version of Fiji to please enable the Fiji-Legacy update site, and instructs users of the new Java 8 version of Fiji to please enable the Java-8 update site.
ClearControl / ClearVolume / ClearCL (Robert Haase, Loic Royer)
- Made Image Quality / Focus measurements from Royer et Al. Nat. Biotechnol. (2016) available as Fiji plugin on a preliminarily update site
- Added support for image quality measurements in regions, tissue depth (rings) or tiled over the whole image
- Fixed bugs regarding discovery of OpenCL files distributed using ClearCLs mechanism
- Adapted ClearControl software to run on another microscope
- Revived code for controlling filter wheels and deformable mirrors
- Merged changes from Max to ClearControl-lightsheet preparing his time stepping procedures
ImgLib2 IJ - (Matthias Arzt)
- Add a wrapper for IJ1 VirtualStack, based on imglib2-caches to support large virtual stacks. (imglib/imglib2-ij#12)
- Refactored, wrappers for ImagePlus (imglib/imglib2-ij#12)
Labkit - (Matthias Arzt)
- Improved Usability of the Labkit plugin. (maarzt/imglib2-labkit)
- Benchmark of different sparse ROI implementations.
ImgLib2 ROIs - (Alison Walter, Tobias Pietzsch, Curtis Rueden)
- Changes related to: imglib2/imglib2-roi#29
- Improved transform operation for ROIs
- Fixed boundary computation for transformed ROIs
- Added knownConstant to ROIs for determining if a ROI will always return
typeparameter for wrappers in
ImageJ-OMERO - (Alison Walter, Josh Moore)
- Added integration test structure (imagej/imagej-omero#69)
- Began adding integration tests (imagej/imagej-omero#70)
- Discussed ROI support and ROI conversions
BigCAT (Philipp Hanslovsky)
- relevant bigcat branch
- Added Painting Functionality
- Multi-scale WIP
- Used for dense annotations but can be used for label creation for classifier training
- Added open dialogs for N5 and HDF5
- Time series
- User guidance in case of invalid input
- Created a mock server to access local file system through http rest api
- Confirmed time series and multi-channel capabilities
- Connected to ilastik backend (Dominik Kutra, Carsten Haubold)
- Tried to re-introduce scenery for 3D rendering together with Ulrik Günther (WIP)
scyjava & imglyb (Philipp Hanslovsky, Curtis Rueden)
- Made plan to separate Java and Python code in imglyb
- Created scyjava python wrapper around pyjnius to allow for runtime resolution of jars/classes that are not on the classpath yet.
- For now: Facilitiate groovy grape, might switch to more generic scijava-grab library later on.
- Removes fat jar requirement of imglyb and will make it easier to distribute
- Currently WIP as jnius.autoclass does not accept custom class loaders as parameter: (kivy/pyjnius#70)
Image Sequence Registration Plugin (Christian Tischer)
- Wrote an ImageJ2 plugin for image sequence registration
- Source code on github
- Installation via new Fiji Update site EMBL-CBA
- The code is written such that additional registration modalities can be readily added
- Current functionality
- Accepts N-dimensional input, allowing the user to select which axes to register
- Translational registration using phase-correlation
- Translational and rotational registration, using phase-correlation for translation and "brute-force" testing of all rotations within user specified range
- Region of interest selection
Mastodon (Jean-Yves Tinevez, Tobias Pietzsch)
- User-assigned tags
- Editable TrackScheme graph
- Revised action handling to allow to switch keymaps
- Navigate-to-branch-child/parent/sibling actions
- Preferences dialog
- Render settings for BDV view
- Keymap configuration
- Code cleanup