Turn a cell movie into tracks you can inspect and export

TrackMate separates detecting objects from linking them through time. Its editing tools let you check which nucleus a path follows before measuring its movement.[5]

This walkthrough follows the current ImageJ documentation, checked on 20 October 2026; we have not processed a movie. Use Fiji and a small, single-channel 2D time-lapse of fluorescent nuclei. Start with a short interval without cell divisions to make the first linking exercise easier to inspect.[5]

Install and calibrate

In Fiji, open Help → Update, then Manage update sites. Enable CSBDeep, Tensorflow, StarDist and TrackMate-StarDist. Close the site list, choose Apply changes and restart Fiji. If the detector is missing afterwards, check that StarDist itself runs before troubleshooting TrackMate.[4][1]

Open the movie and inspect Image → Properties. Put the images in the time dimension, not a stack of Z slices, and enter the recorded pixel size and frame interval. Save the calibrated image as TIFF. Launch Plugins → Tracking → TrackMate and check its start panel; Refresh source imports metadata corrections.[2]

Find the nuclei, then connect them

Select StarDist detector and Preview the current frame. Inspect several frames, especially crowded regions. This built-in detector uses fixed thresholds and a model for fluorescent nuclei; a poor match to your images may require a separately trained model. Choose Next to process the sequence.[1]

Review the spot-filter panels against the image before removing small or dim detections. For this initial interval, choose Simple LAP tracker. Set its linking distance from the largest plausible movement between consecutive frames, in the calibrated spatial units. Keep gap closing small enough to inspect any proposed bridge across a missed detection.[2]

Do not increase the distance merely to make every path continuous. If two neighbouring nuclei cross, an apparently smooth line can still switch identity. Follow those ambiguous passages frame by frame before treating the measurements as belonging to one cell.

Correct the links and export the work

Open TrackScheme. To remove a false connection, select its link and press Delete. To connect the right detections, enable TrackScheme’s linking tool and drag from the source spot to its target. In the image view, hovering over a missed nucleus and pressing A adds a spot; D removes a false one.[3]

Use the Tracks button to open the data window. Export separate CSV files for Spots, which describe detections, and Edges, which describe the links between them. Keep their identifiers so measurements can be traced back to the image.[1]

Also press Save in TrackMate to keep the XML session. It stores the tracking data and a reference to the source image, not the image pixels. Retain the TIFF alongside it.[2]

Open the CSVs and check the reported spatial and time units against your acquisition record. Pick one reviewed path and locate its entries before analysing the whole dataset. You now have measurements that can be traced back to the movie, with the editable session available when a doubtful link needs another look.

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