I released the first version of BTrackmate today with the update site of MTrack. It is intended to do tracking with either an integer label image or a CSV file of cell attributes which this notebook creates:
If you want to track cells inside a region you can load a Mask image along with Raw and integer label segmentation, the program then computes intensity, size, location and makes a CSV file with Fiji appended before the filename in the folder of the Raw image.
This step is to increase the overall speed of the workflow, after this step you can upload just the Raw image along with the CSV as I show here:
This also saves the memory overload (you can skip inputting the segmentation image unlike I did when making the video). SInce the localization of particles is already solved I skip the Trackmate panels doing that using DoG or other detectors and you directly enter the tracking panel with LAP and Kalman Filter trackers as options.
After doing the tracking the users also have the option of saving the xml and loading it in Napari for track visualization and computing some information from the tracks using this NotebookVisualization
I hope you find this useful and send us some feedback. The source code is here BTrackMate