FLIMKit

Plugins / FLIMKit / Fiji Bridge · edit on GitHub

Fiji Bridge

The Fiji plugin is the other client of the FLIMKit bridge. It moves images and ROIs between FLIMKit and Fiji's ROI Manager, and runs FLIMKit's fits from Fiji. It was written by Zhen Yuan Yeo (10.5281/zenodo.21951612).

Installing the Fiji plugin

Two things, and the plugin does nothing without both.

  1. pip install flimkit-bridge into the environment FLIMKit runs from.
  2. In Fiji, Help > Update..., then Manage update sites. Tick FLIMKit-Bridge, or if it is not listed, Add unlisted site with the name FLIMKit-Bridge and the URL https://sites.imagej.net/FLIMKit-Bridge/. Apply changes and restart Fiji.

The updater keeps it current, so that is the route to prefer. Failing that, put flimkit-fiji-bridge-<version>.jar from the releases into Fiji's plugins/jars/ folder, which is where the update site puts it.

Fiji 2.16 or newer is required, with its bundled JDK 21. An older Fiji fails to load the plugin with UnsupportedClassVersionError, or Module javafx.base not found, and neither message says to upgrade Fiji.

Using the Fiji plugin

Ten commands appear under Plugins > FLIMKit:

Fiji Plugins > FLIMKit

Command What it does
Connect Pair with the running FLIMKit or a headless flimkit-bridge
Fetch FLIMKit images Pull the current intensity and lifetime images, with their units in the calibration
Fetch ROIs from FLIMKit Load FLIMKit's Regions table into the ROI Manager
Fit ROI decays... Fit the decay summed over each ROI
Fit a z-stack... Fit a folder of region_zN.ptu slices as one FOV
Fit per-pixel lifetimes... Run a per-pixel fit and return the maps
Open FLIM file... Open .ptu, .sdt, .photons and the other formats FLIMKit reads
Phasor plot... An interactive phasor window
Send ROIs to FLIMKit Push the ROI Manager contents back as GeoJSON
Stitch and fit a mosaic... Stitch a multi-position acquisition and fit it

File > Open handles the FLIM formats directly too.

Connect reports the bridge and FLIMKit versions it found:

Fiji connected

Fetch FLIMKit images opens two windows, FLIMKit intensity (16-bit photon counts) and FLIMKit lifetime (32-bit, ns). This is the Series008 z-stack from Step 14 with the mpl-viridis lookup table applied in Fiji:

Lifetime image fetched into Fiji

Only fitted lifetime and photon-count intensity cross. Raw per-pixel decay histograms do not; that would need a separate data and metadata contract. Fiji rejects ROIs from an image of different dimensions rather than silently rescaling them, and registration stays a Fiji-side job.