FLIMKit-Bridge provides direct image and ROI exchange between FLIMKit and Fiji (ImageJ), and brings FLIMKit’s tools – fitting, phasor analysis, and stitching – to Fiji.
Installation
In the Fiji Updater, tick FLIMKit-Bridge. If it is not in the list yet, use Add unlisted site with name FLIMKit-Bridge and URL https://sites.imagej.net/FLIMKit-Bridge/.
FLIMKit-Bridge needs the flimkit-bridge server running in the background to talk to Fiji:
- If you already have FLIMKit’s desktop app open, you’re set – the bridge starts automatically and its status is shown under
Tools > FLIMKit Bridge.... - Otherwise (e.g. a headless machine, or Fiji-only use), run:
pip install flimkit-bridge
flimkit-bridge
How it works
Once connected, FLIMKit-Bridge adds commands under Plugins > FLIMKit:
- ROIs – draw a region of interest in Fiji as usual, then Send ROIs to FLIMKit to push the ROI Manager contents back as GeoJSON (no image is returned, just a confirmation). Fetch ROIs from FLIMKit does the reverse: it loads FLIMKit’s Regions table into Fiji’s ROI Manager as new ROIs.
- Images – Fetch FLIMKit images pulls the current intensity and lifetime images across as float32 TIFFs, opened directly as Fiji windows, with their measurement units carried in an
X-FLIMKit-Value-Unitheader. - Fitting – Fit per-pixel lifetimes… runs a per-pixel exponential fit and returns the resulting lifetime maps as new Fiji images. Fit ROI decays… sums the decay within each ROI first and returns the fit results per region – useful when per-pixel data is too noisy.
- Phasor plots – Phasor plot… opens an interactive phasor window for the current image; this is a visualization, not an exported image.
- Stitching – Stitch and fit a mosaic… stitches a multi-position/tiled acquisition and returns the fitted result across the assembled mosaic.
Supported file formats
Fitting + phasor: PicoQuant PTU (.ptu), Becker & Hickl SDT (.sdt), Photonscore LINCam (.photons), PicoQuant BIN (.bin), PicoQuant PHU (.phu), SimFCS B&H (.b&h), SimFCS BHZ (.bhz), ImSpector FLIM TIFF (.tif, .tiff), ISS Vista TDFLIM (.iss-tdflim, .tdflim), FLIM LABS imaging (.json), ISS time-tag (.tagtime, .tagchannel, .tagdecay).
Phasor only: ISS FD-FLIM (.ifli), SimFCS referenced (.ref, .r64), PhasorPy OME-TIFF (.ome.tif), FLIM LABS phasor (.json).
Intensity only: ISS intensity image (.ifi).
Measured IRFs can be supplied as .xlsx, .csv, or .pck files.
Requirements
- Fiji 2.16 or newer with bundled JDK 21
- Python 3.12 or newer (only needed for the standalone bridge)
