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
Topics / Technical Discussions
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.