COBA ImageJ/Fiji 2020 summer progress report and fall roadmap

Hi ImageJ/Fiji teams & interested parties!

Continuing from our summer 2020 roadmap, here is a progress report and roadmap of the @eliceiri/LOCI group’s technical efforts under the COBA center on ImageJ & Fiji development.

Summer progress report

  1. In late June, our main ImageJ web server was compromised. Hackers installed web shells, and the entire contents of were wiped out. (Fortunately, we keep regular backups.) We spent July and August heavily focused on strengthening our server infrastructure. We have stopped using CMS software on our public-facing sites, migrating away from Drupal and MediaWiki in favor of static content. All site configuration is now versioned in a private git repository. We wiped, upgraded, and reinstalled our primary web server, and distributed hosted sites across five different machines, divided by needed functionality. You can peruse more details of the migration on this thread.

  2. In late July, we completed the pom-scijava 29 release and made a corresponding release of ImageJ2 and release of Fiji, including latest versions of all bundled components. These were large updates with lots of changes. Unfortunately, we don’t have a robust system in place yet for changelog summaries across all of Fiji’s components and plugins—although this is something we are hoping to change for the next major release.

  3. Our sudden migration away from MediaWiki led us to temporarily convert to read-only static content, and exert a concentrated push toward the new GitHub-Pages-based Huge thanks to @frauzufall and @elevans for their hard work on it during July and August. :beers: The new site is still not ready to replace, but community review and editing is now possible. See this thread for more on the new website as it develops.

  4. Similarly, the site was also migrated to GitHub Pages. Initially, I did it hurriedly and incompletely; big thanks to @turekg for picking up the pieces and completing the remainder of the migration.

Fall projects

Now that our servers are back on track, we are resuming development of the several projects including:

  1. [Sep] ImageJ Launcher support for JBRSDK8 (fiji/fiji#240)

    • Needed for JavaFX support (e.g. for FLIMJ)
    • Includes quality-of-life improvements and bug-fixes like HiDPI support on Windows
  2. [Sep-Oct] Update PyImageJ component stack and release 1.0.0

    • Convert PyImageJ component stack from PyJNIus to JPype. (scyjava is already working; see this branch)
    • Release 1.0.0 versions of imglyb, scyjava and jgo to PyPI and conda-forge
    • Test 1.0.0 component stack on clean machines across all platforms
    • Release PyImageJ 1.0.0 and announce to community
    • Complete and submit PyImageJ paper
  3. [Oct] ImageJ-OMERO update (scijava/pom-scijava#122) to support OMERO 5.5 and 5.6 in conjunction with pom-scijava 29.

  4. [Nov] Complete the transition of to GitHub Pages.



  • :palm_tree: ON VACATION UNTIL OCTOBER 5 :palm_tree: For real this time! :wink:
  • Work on ImageJ-OMERO, pyimagej, and after I return.


  • Complete the update to JBRSDK8.
  • Work with @elevans towards PyImageJ 1.0.0.
  • Cover any urgent technical issues while @ctrueden is away.


  • Work with @hinerm towards PyImageJ 1.0.0.
  • Work with @smgriffin2 toward completion of the new


  • Continue work on imagej-ops2 in scijava/incubator.
  • Modularize that codebase and work toward 1.0.0 component releases and Ops paper.