Difference between revisions of "2017-12-04 - Fiji + KNIP hackathon"

(Added things Robert and Loic did during the hackathon)
m (TrackMate & MaMuT (Ulrik Gunther, Kyle Harrington, Jean-Yves Tinevez))
 
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* Revived code for controlling filter wheels and deformable mirrors
 
* Revived code for controlling filter wheels and deformable mirrors
 
* Merged changes from Max to ClearControl-lightsheet preparing his time stepping procedures
 
* 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. ({{GitHub | org=imglib | repo=imglib2-ij | pr=12 | label=imglib/imglib2-ij#12}})
 +
* Refactored, wrappers for ImagePlus ({{GitHub | org=imglib | repo=imglib2-ij | pr=11 | label=imglib/imglib2-ij#12}})
 +
 +
=== Labkit - (Matthias Arzt) ===
 +
* Improved Usability of the Labkit plugin. ({{GitHub | org=maarzt | repo=imglib2-labkit | label=maarzt/imglib2-labkit}})
 +
* Benchmark of different sparse ROI implementations.
 +
 +
=== ImgLib2 ROIs - (Alison Walter, Tobias Pietzsch, Curtis Rueden) ===
 +
* Changes related to: {{GitHub | org=imglib | repo=imglib2-roi | pr=29 | label=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 <code>false</code> or <code>true</code>
 +
** Removed <code>type</code> parameter for wrappers in <code>Masks</code> static methods, <code>BoolType</code> by default
 +
 +
=== ImageJ-OMERO - (Alison Walter, Josh Moore) ===
 +
* Added integration test structure ({{GitHub | org=imagej | repo=imagej-omero | pr=69 | label=imagej/imagej-omero#69}})
 +
* Began adding integration tests ({{GitHub | org=imagej | repo=imagej-omero | pr=70 | label=imagej/imagej-omero#70}})
 +
* Discussed ROI support and ROI conversions
 +
 +
=== BigCAT (Philipp Hanslovsky) ===
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* [https://github.com/saalfeldlab/bigcat/commits/javafx-generic-listeners relevant bigcat branch]
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* 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
 +
** Auto-discovery
 +
** Channels
 +
** Time series
 +
** multi-scale
 +
** User guidance in case of invalid input
 +
* Created a mock server to access local file system through http rest api
 +
** [https://github.com/hanslovsky/n5-rest hanslovsky/n5-rest]
 +
* 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 {{Person|Skalarproduktraum}} (WIP)
 +
 +
=== scyjava & imglyb (Philipp Hanslovsky, Curtis Rueden) ===
 +
* Made plan to separate Java and Python code in imglyb
 +
* Created [https://github.com/scijava/scyjava scyjava] python wrapper around [https://github.com/kivy/pyjnius 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: ({{GitHub | org=kivy | repo=pyjnius | issue=316 | label=kivy/pyjnius#70}})
 +
 +
=== Image Sequence Registration Plugin (Christian Tischer) ===
 +
* Wrote an ImageJ2 plugin for image sequence registration
 +
* Source code on [https://github.com/tischi/fiji-plugin-imageRegistration 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
 +
 +
 +
=== TrackMate & MaMuT (Ulrik Günther, Kyle Harrington, Jean-Yves Tinevez) ===
 +
* Prototype of a 3D viewer for [[TrackMate]] and [[MaMuT]] based on [[SciView]] and [[Scenery]].
 +
 +
  
 
[[Category:News]]
 
[[Category:News]]

Latest revision as of 05:41, 9 January 2018

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.


https://gitter.im/fiji/hackathon_dd_2017


Voluntary hackathon calendar

https://tinyurl.com/ybjcq9qw

Hackathon google doc

https://docs.google.com/document/d/1h4uCt4PAEdeGQQwwVZC73o_Anq6-AI2KZiSzxY8kWng/edit

Hackathon on Twitter (#hackdd17)

https://twitter.com/hashtag/hackdd17?vertical=default&src=hash

Technical Discussions

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?

BigDataViewer

  • There is a fork of BigDataViewer for JavaFx. [1]
  • 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

ImageJ/Fiji parallelization

  • 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

Hackathon Progress

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
  • worked on a new JavaScript client with enhanced UI, making use of the Angular framework
  • 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)

ImageJ Ops - (Curtis Rueden)

ImageJ Legacy - (Curtis Rueden)

ImageJ Launcher - (Curtis Rueden)

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)

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 false or true
    • Removed type parameter for wrappers in Masks static methods, BoolType by default

ImageJ-OMERO - (Alison Walter, Josh Moore)

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
    • Auto-discovery
    • Channels
    • Time series
    • multi-scale
    • 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


TrackMate & MaMuT (Ulrik Günther, Kyle Harrington, Jean-Yves Tinevez)