flimkit-bridge

The local HTTP server that FLIMKit image analysis clients talk to.

Two add-ons use it. The QuPath extension and the Fiji add-on are both clients of this one server, so a fix here reaches both and neither carries its own copy of the API.

It started inside the QuPath add-on and moved out once there were two clients. The wire protocol it speaks was designed and first implemented in flimkit-fiji-bridge by Zhen Yuan Yeo (https://doi.org/10.5281/zenodo.21951612).

Running it

The server starts with FLIMKit. Tools > FLIMKit Bridge... shows its address and whether anything has connected.

It also runs without the desktop app, which is what you want on a headless machine or when QuPath or Fiji is the only front end:

pip install flimkit-bridge
flimkit-bridge

--port and --token are there if you need them, --force takes over from a bridge that has been left running, and --no-announce serves alongside one instead.

Pairing

The server writes its address and a generated token to ~/.flimkit/bridge.json, and clients read that file, so there is nothing to type in. Each start mints a new token, so a client re-reads the file before every call.

It writes ~/.flimkit/qupath-bridge.json alongside it, carrying the same address under the older protocol name. QuPath extensions built before the server moved out check for that name and stop pairing without it. The second file goes when those versions are retired.

Versions

GET /v1/status reports protocol_version, bridge_version and flimkit_version. A client checks protocol_version, which is what governs whether the two can talk. bridge_version is for display: the server and each client version independently now, so a difference between them is ordinary rather than a problem.

Security

The server listens on 127.0.0.1 only, and refuses any request whose Host header is not localhost, which stops a web page reaching it by resolving its own hostname to your machine. Every endpoint except the status check requires the token.

Both programs therefore have to be on the same machine. If they are not, forward the port over SSH rather than exposing it:

ssh -L 8765:127.0.0.1:8765 you@the-flimkit-machine

Licence

MIT. See LICENSE.md.