v0.4.0

Expert fit settings reach QuPath. The fit dialog is built from the bridge's own schema, so every setting FLIMKit offers appears without a Java change, and the advanced ones are behind a disclosure. Phasor cursors report lifetimes rather than only positions.

A region's decay is now the sum of every pixel the region covers. min_photons was applied per pixel before that sum, which on a sparse field threw away almost everything: 244 photons of 8,206 at half a photon per pixel, reading 0.56 ns low against a known 1.7644 ns. It is a per-pixel setting and no longer appears in the ROI fit dialog. On a bright field the change is under 0.02 ns; on a photon-starved one it is the difference between a fit and a wrong number.

Pile-up in the forward model reaches a region fit. fit_masked_decay took the sync count and dropped it, so the setting was silently a no-op for every ROI fit. The count is now scaled to the fraction of the field the region covers, since a region that is a sixteenth of the image saw a sixteenth of the pulses. Handing it the whole-image count instead understates pile-up by that factor and lands back on the uncorrected answer.

CITATION.cff matches the Zenodo record, which listed Hunt and Akram while the citation file listed Hunt alone. A version test now holds it to the same version as the gradle build and EXTENSION_VERSION.

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Two halves, one on each side.

The Python half comes from PyPI, into the environment FLIMKit runs in:

pip install flimkit-qupath-bridge

That pulls FLIMKit with it. The bridge then starts with FLIMKit and adds a Send to QuPath button to the ROI panel. flimkit-bridge is on the path as well, for the server without the FLIMKit window.

The wheel and sdist are attached below for anyone installing offline, or into ~/.flimkit/plugins/.

QuPath extension: drop qupath-extension-flimkit-bridge-*.jar into QuPath's extensions directory, normally ~/QuPath/v0.7/extensions. It appears under Extensions > FLIMKit bridge.

Co-registration needs the QuPath alignment extension, which QuPath does not ship. Without it you can still exchange images and ROIs, but only between images that already share a coordinate system.

Requires QuPath 0.7.0 or newer, Python 3.12 or newer, and FLIMKit 0.13.0 or newer.