Difference between revisions of "2018-12-06 - I2K 2018 Dresden Hackathon"

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From Monday, December 3, 2018 through Friday, December 7, 2018, the [https://mpi-cbg.de/ Max Planck Institute of Molecular Cell Biology and Genetics] hosts ~10 developers at the [http://www.csbdresden.de/ Center for Systems Biology] in Dresden, Germany for a [[hackathon]] to develop KNIME Image Processing and [[ImageJ2]]/[[Fiji]] core infrastructure and [[plugins]].
 
From Monday, December 3, 2018 through Friday, December 7, 2018, the [https://mpi-cbg.de/ Max Planck Institute of Molecular Cell Biology and Genetics] hosts ~10 developers at the [http://www.csbdresden.de/ Center for Systems Biology] in Dresden, Germany for a [[hackathon]] to develop KNIME Image Processing and [[ImageJ2]]/[[Fiji]] core infrastructure and [[plugins]].
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Gitter channel: https://gitter.im/juglab/Hack1812
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== Topics / Technical Discussions ==
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 +
=== TensorFlow (Debo, Curtis, Benny) ===
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* 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) ===
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 +
* 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
 +
 +
=== Governance ===
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* 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)
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* Update fiji.sc, imagej.net/Fiji, etc. with revised maintainership info
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Google Scholar: citation count badges on wiki pages
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* What to do about NanoJ using google analytics -- i.e. should we have usage stats?
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** [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
 +
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=== Wiki ===
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 +
* 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) ===
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* Get it merged to scijava-common / scijava-ui-swing
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* https://forum.image.sc/t/error-noclassdeffounderror-net-imagej-table-table/21369/7
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=== Curtis ===
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* 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
 +
 +
=== Other ===
 +
* 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)

Latest revision as of 09:10, 17 December 2018

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

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

Governance

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

Wiki

  • 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)

Curtis

  • 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

Other

  • 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)