Use apps inside napari, Fiji and QuPath
Some apps declare tools: scientific functions with typed inputs. A plugin for your image software turns each tool into a form, runs it, and puts the result back into your software: images become layers or windows, outlines become overlays, points become point ROIs, numbers go to a log or a table.
The tool runs in the app's own Python environment, in a separate process. Your image software never imports the app's packages, so apps with conflicting dependencies can live side by side. Fiji (ImageJ) and QuPath need no Python at all; napari is itself a Python program, and its plugin is installed into the environment where napari runs.
Under heavy construction
The napari, Fiji and QuPath plugins are untested and unlikely to be stable. Expect bugs, missing features and changes without notice. Each plugin's own guide says what stage it is at.
Three steps
- Install the app you want to use. The installer registers the app on your computer, which is how the plugins find it.
- Install the plugin for your software: napari, Fiji or QuPath.
- Open it:
-
napari: Plugins > LabConstrictor tools
- 
Fiji: Plugins > LabConstrictor > LabConstrictor Tools...
- 
QuPath: Extensions > LabConstrictor tools...
A first run needs step 1: an installed LabConstrictor app that declares tools. With none registered, the plugin has no app to list.
Then pick an app and a tool. Parameters become fields with their ranges and units, and each image input accepts an image you have open or a file.
Help with testing is welcome: the human test protocol says what to try.
Very long texts on Windows
A terminal line copied from a plugin (the "copy as command" button) carries your parameter values. On Windows a line longer than about 32,000 characters cannot start, because of the operating system's command-line limit, so a text parameter longer than that cannot be run from a copied terminal line. Run such a text from the plugin's form, or from the notebook or worker path (the Python snippet), which have no such limit.
Check that everything works
Install the LabConstrictor Playground app and press Check everything. It tests your machine and every plugin feature, and writes a report you can attach to an issue.
Make your own tools
App authors declare tools once, in Python, and get all of this without writing any interface code. See the authoring guide.