Articles tagged with imagej

Manage ImageJ update site on localhost with git


I've discovered that one can use the file: "protocol" to manage ImageJ update sites that are actually a git repository on the local filesystem. This means that I can then have the update site pull the changes from somewhere rather than have ImageJ push the changes to the remote update site. This reduces the need for direct access to the server with the overall goal being automating its deployment.


To make a new release of SIMcheck, an ImageJ plugin, I do the following dance:

  1. build new release of SIMcheck;
  2. install it on a fresh local copy of Fiji;
  3. use the ImageJ updater to update the remote update site.

While most projects have their update site on, we host the SIMcheck update site on one of our own servers — the Micron downloads site — together with some mirrors for other ImageJ update sites. I like to own my infrastructure and I like it distributed [1].

Anyway, I was never very happy with step 3 of this dance, namely the part where ImageJ pushes changes directly to the public website. This is in large part because I'm not happy with our the current setup. I don't like having to access the downloads server to upload files. I would much rather have them somewhere else and then configure the server to fetch/mount the files from that somewhere else. I also want to have the downloads site under version control and integrity checks. My plan is to use git-annex but there's always a lot of work to do and since infrastructure work is never urgent it never gets done.


While restructuring our servers is not going to happen overnight, I'm doing it one step at a time. For starters, I created a git repository with the SIMcheck update site. The plan now is to set up the downloads site to serve that git repository and only have to specify the git hash to deploy on the ansible playbook.

But the ImageJ updater only makes changes on remote servers. From its "documentation":

If you have an own server or web space with WebDAV, SFTP or SSH access, you can create a directory in that web space and initialize it as an update site, too.

I could set one of those services locally but seems too much work when the things are already local. So despite the documentation I tried to use file: as "host" and it worked just fine. This is how it looks like on the ImageJ update site manager:

How the configuration looks like on the ImageJ update site manager.

So my dance now is as follow:

  1. download a fresh copy of ImageJ;
  2. configure the updater with a SIMcheck update site that is the local git clone;
  3. install new version of SIMcheck;
  4. update the SIMcheck update site (local git clone) with the new version with the ImageJ updater;
  5. commit and push the changes to the SIMcheck update site;
  6. pull the changes on the public server.

Which at the command line, roughly translate into:

$ wget
$ unzip
$ cd
$ ./ImageJ-linux64 --update update
$ ./ImageJ-linux64 --update add-update-site SIMcheck-local \
      file:/home/carandraug/src/SIMcheck-update-site/ \
      file: \
$ ./ImageJ-linux64 --update update
$ mv PATH-TO-SIMCheck-REPO/target/SIMcheck_-1.3.jar plugins/
$ rm plugins/SIMcheck_-1.2.jar
$ ./ImageJ-linux64 --update upload \
      --update-site SIMcheck-local \
$ cd ~/src/SIMcheck-update-site
$ git add plugins/SIMcheck_-1.3.jar-20210121203119
$ git add db.xml.gz
$ git commit -m "SIMcheck release 1.3"

Future Ideas

I think it might be interesting to have something like this for automating releases. An automation server can be triggered to build new releases and push them to a git repository for each update site. A site that serves those update sites can be configured to pull and serve a specific commit for each update site.

[1]It's not only me. The ImageJ project itself seems interested in having mirrors of its resources. If you can set a mirror, checkout the thread Who can mirror ImageJ online resources?