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Install the Fiji plugin

One Fiji (ImageJ) command runs the tools of every installed LabConstrictor app, with a dialog generated from each tool's declaration.

Under heavy construction

This plugin is untested by people on real machines and unlikely to be stable. Expect bugs, missing features and changes without notice. Do not rely on it for work you cannot redo.

The plugin is installed from a GitHub release (a jar, or a script with its helper files); there is no Fiji update site yet. Releases are pre-releases (alpha): take the newest one on the Releases page.

What you need

  • Fiji.
  • At least one LabConstrictor app installed on your computer. The app's installer registers it, which is how the plugin finds it. The app needs labconstrictor-tools 0.3.0a1 or newer (tag v0.3.0-alpha.1): an app with an older one is left out of the list, with a sentence in the Log window.
  • Apps declare which hosts list them (hosts: in their labconstrictor-app.yaml); the rule is a binding rule in Tools 0.3.0a1 (feature app_hosts_v1; PROTOCOL.md section App hosts); Napari, Fiji and QuPath all honour it (this host since PR #47). Apps without a declaration, i.e. installed with an installer from before template 0.1.18, are listed in every host and the Log says so ("declares no hosts"); installers pass the hosts from template 0.1.18 (merged; the five apps of the alpha.3 test set carry it). Intended for Fiji: Playground, NucleiSky, Guess the Condition and VLab4Mic. CellTracksColab is not listed in any host.
  • Nothing to build: no Java or Maven is needed to install.

Install

The full install page for the apps and all three hosts is Tools docs/INSTALL.md. For Fiji:

  1. Download labconstrictor-fiji-<tag>.jar from the Releases page (<tag> is the release tag; take the latest release).
  2. Put it into Fiji.app/plugins/ (not a subfolder; remove an older labconstrictor-fiji-*.jar) and restart Fiji.
  3. Run Plugins > LabConstrictor > LabConstrictor Tools....

No-jar alternative: the same release has labconstrictor-fiji-script-<tag>.zip. It holds the script LabConstrictor_Tools.groovy and the lib folder it needs (the script alone stops with a message). Unzip it so both sit in Fiji.app/scripts/Plugins/LabConstrictor/; the menu entry is then Plugins > LabConstrictor > LabConstrictor Tools (no dots). Macro calls need the jar. Install one of the two, not both (with both, the menu lists the tool twice).

SHA256SUMS in the release lists the checksums of the jar and the zip. Every release jar is installed in Fiji and run on GUI cases before it is attached. The release gate is Linux; Windows and macOS (Apple silicon) get a best-effort check in the release run that can fail without blocking a release, and nobody has used the plugin on those systems by hand yet.

Testing the plugin and reporting back: the human test protocol and its record sheet (same PR).

Open it

Choose Plugins > LabConstrictor > LabConstrictor Tools... (without the dots if you installed the script). Pick an app and a tool, fill in the dialog, and press OK.

When the run ends, the same tool's dialog opens again for the next run, with the values you used. Change what you need (the next guess, another parameter) and press OK again. Press Cancel when you are done. - An image's "(or file)" field starts empty again, so the next run uses the open image unless you choose a file again. - A field the tool marks "clear after run" (a guess, for example) goes back to its default after a run that worked. - Lists that come from another tool are asked again, so they are up to date. - While the dialog is open you cannot use other Fiji windows. To zoom or open another image, press Cancel, then start the tool from the menu again.

< Back (beside OK and Cancel) takes you one window back: from a tool's dialog to the list of tools, and from the list of tools to the list of apps. If you pick the same tool again, its dialog shows what you had typed. A list with only one entry is skipped, so Back goes past it.

The next time you open the menu, the app and tool choosers start on the app and tool you picked last.

A first run needs an installed LabConstrictor app that declares tools. If none is registered, Fiji shows the message "No LabConstrictor apps are registered" and stops.

  • Each image input has a chooser for an open image and an "(or file)" field. A file wins.
  • Results open as image windows, a Results table, ROIs or overlays on the image, or lines in the Log window.
  • Press Esc to cancel. A progress bar shows while a tool runs.
  • After every run, the Log window shows the terminal line and the Python snippet that repeat it outside Fiji.

If something does not work

  • A failure dialog shows the tool's error, the worker's last output and where the log is: ~/.labconstrictor/logs/labconstrictor.log.
  • labconstrictor-tools doctor shows which apps are registered and why one might be skipped.
  • No menu entry: the jar is not directly in Fiji.app/plugins/, or Fiji was not restarted.
  • Pixel-size field: there is no "use the image's calibration" button; the field follows the image by itself until you type a value. Typing the value the box already shows cannot be detected in a Fiji dialog, so the field is cleared and the run is blocked with a message; a wrong value is never sent.

Source, macro replay (needs the jar) and issues: LabConstrictor-Fiji.

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