Installation

Installation

Two halves, one on each side. Both are attached to every release.

FLIMKit side

Install the wheel into the environment FLIMKit runs in:

pip install flimkit_qupath_bridge-0.1.0-py3-none-any.whl

Or, if you are using the compiled app which has no pip, drop the .whl straight into ~/.flimkit/plugins/. FLIMKit puts it on the import path before it scans for add-ons.

User plugins are off until you say otherwise. Open Help > Plugins... and press Enable, or set plugins.allow_user_plugins to true in ~/.flimkit/config.json. It takes effect on the next start.

QuPath side

Drop the jar into QuPath's extensions directory:

~/QuPath/v0.7/extensions/qupath-extension-flimkit-bridge-0.1.0.jar

Restart QuPath. The bridge appears under Extensions > FLIMKit bridge.

For co-registration

Install the QuPath alignment extension as well. QuPath does not ship it, and neither 0.6.0 nor 0.7.0 includes interactive image alignment without it.

Without it you can still exchange images and ROIs, but only between images that already share a coordinate system.

Checking it worked

Start FLIMKit. The console reports the address it bound and where it wrote the pairing details:

[QuPath bridge] listening on http://127.0.0.1:8765
[QuPath bridge] details written to /Users/you/.flimkit/qupath-bridge.json

In QuPath, Extensions > FLIMKit bridge > Connect should report Connected to http://127.0.0.1:8765 without asking you anything.