Exporting cellprofiler rois and track labels

Does anyone know of a way to export cellprofiler segmentation ROIs and track labels into another software such as Fiji?


You’re probably looking for the ConvertObjectsToImage module, set to ‘uint16’ mode, followed by SaveImages for ROIs. Alternatively if you use the output images from the TrackObjects module the labels should persist across frames, although this won’t work for the LAP tracking method since LAP labels aren’t assigned until the end of the run.

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