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FLIMKit QuPath bridge

Direct image and ROI exchange between FLIMKit and QuPath.

FLIMKit serves its intensity and lifetime maps and its ROIs over a loopback HTTP connection. QuPath reads and writes them from inside a live session, so you work with the image you have open and the annotations you have drawn, rather than exporting files and importing them again.

• Installation
• Using the bridge
• Co-registration
• Protocol
• Troubleshooting

What it is for

Draw ROIs on a brightfield or mIF image in QuPath, where the annotation tools and cell detection are strong, then send them to FLIMKit to get lifetimes out of the matching FLIM field of view. The FLIM images can also go the other way, into the QuPath project, so they sit beside the brightfield in the viewer grid.

Requirements

QuPath	0.7.0 or newer
FLIMKit	0.11.0 or newer
Python	3.12 or newer
Co-registration	QuPath alignment extension, installed separately

Both programs have to be on the same machine. See Protocol for why, and for the SSH tunnel if they are not.

Status

v0.1.0. The transport, ROI exchange in both directions and the project import are covered by tests, including against real FLIMKit sessions on a Leica SP8 FALCON. The menu items and the FLIMKit button have not yet been driven by hand in a live session.