Track dense cells from maps

The ITASC ingredient board with Ultrack, Ultrack correction, EpiCure editing, and Core lit; the Cellpose maps it consumes and every other piece dashed.

itasc-tracking ships the Ultrack nucleus tracker and both its correction tools, on the shared Core. It consumes the foreground and contour maps you supply. Solid chips are shipped; dashed are the rest of the family.

The ITASC ingredient board with Ultrack, Ultrack correction, EpiCure editing, and Core lit; the Cellpose maps it consumes and every other piece dashed.

itasc-tracking ships the Ultrack nucleus tracker and both its correction tools, on the shared Core. It consumes the foreground and contour maps you supply. Solid chips are shipped; dashed are the rest of the family.

itasc-tracking is the nucleus tracking stage on its own, run inside the napari viewer. It takes the foreground and contour maps Cellpose produced and turns them into tracked, correctable nucleus labels, using the Ultrack solver. Reach for it when you already have those maps and want tracks without the full pipeline’s project folder.

This is Stage 2 of the full app, lifted out on its own. Everything it does, from atom extraction through the solve to the correction pass, works exactly as it does there, so that page is the explanation: read it for what each button does and how to correct the tracks.

The Ultrack Segment + Track panel in napari, with foreground, contours, and output paths set.

The Ultrack Segment + Track panel. The three fields point it at the two input maps and the folder for its results; the buttons below run the stages top to bottom.

The one difference

The full app reads and writes through a project folder, one position at a time. This tool takes files instead: point Foreground at the foreground map, Contours at the contour map, and Output dir at a folder for the results (it defaults to the foreground file’s folder). The two inputs can have any name and live anywhere. Run the stages top to bottom, correct the tracks, and the results land in the output folder.

Install

pip install "itasc-tracking[solve]"

The [solve] extra adds the Ultrack solver, imported only when you build the database or solve; correction-only use does not need it. To run it as a napari app instead of installing into your own environment, the install guide sets up napari and the tool together.

For scripting

The headless backend lives under itasc.tracking_ultrack (atoms, database, linking, solving, export, correction) and itasc.correction (label edits), Qt-free and importable without the full app. The full-app guide covers the pipeline this stage sits in.