v0.6.1

Fixes the pixel counts in the phasor window.

QuPath extension: drop qupath-extension-flimkit-bridge-0.6.1.jar into QuPath's extensions directory, normally ~/QuPath/v0.7/extensions, replacing the 0.6.0 jar, or update it from Extensions > Manage extensions if you added the catalog. The server side is unchanged: pip install flimkit-bridge.

What changes

• Phasor cursors count the pixels the plot shows. The window drew every pixel with a mean of 0.01 photons per bin, then asked for cursor counts at 1.0, so on a typical image almost nothing inside a cursor was counted. On a 1024 x 1024 PTU at binning 4, a cursor on the densest part of the cloud reported 43 px where it now reports 10,854, and one on a visibly populated area went from 0 to 543. The window no longer sends a floor, so the counts, the lifetimes they report and the annotations Create annotations makes all use the plot's own.

Requires QuPath 0.7.0 or newer and FLIMKit 0.13.0 or newer.

v0.6.0

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.

v0.5.0

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.

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.

---

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.

v0.3.0

Per-pixel fitting can be run from QuPath, and the lifetime maps arrive in the project as one image with a channel per map in nanoseconds. Annotations get a mean and a median per map.

Tail fits are selectable, the advanced fit settings are reachable, and the dialog's number fields take typing.

tile_fit is the default pipeline, per-pixel fits use the GPU, and the decode cap scales with the machine rather than sitting at 2 GiB.

QuPath warns when the extension and the bridge are different versions, and survives a bridge restart without needing Connect again.

See the README for the endpoints.

---

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 0.12.0 or newer.

v0.2.0

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 0.12.0 or newer.

v0.1.1

Two things to install, one on each side.

FLIMKit add-on: install the wheel into the environment FLIMKit runs in, or drop it in ~/.flimkit/plugins/. The bridge then starts with FLIMKit and adds a Send to QuPath button to the ROI panel.

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 a FLIMKit with the plugin bindings and startup hooks.

v0.1.0

Two things to install, one on each side.

FLIMKit add-on: install the wheel into the environment FLIMKit runs in, or drop it in ~/.flimkit/plugins/. The bridge then starts with FLIMKit and adds a Send to QuPath button to the ROI panel.

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 a FLIMKit with the plugin bindings and startup hooks.