Calling tp.link on pre-segmented objects

[Ciro1990]

Hello,

I was wondering if it is possible to call the tp.link function on pre segmented objects (i.e. on Cellpose masks). I would like to try Trackpy on live imaging of cells (brightield) which have been segmented already with Cellpose.

Thanks! Ciro

[nkeim]

I'm not familiar with that package. What kind of output does it produce that link would need to process? (Is it different from an array of coordinates?)

[Ciro1990]

Th output of Cellpose is an array of labels with the same dimension of the image, in which every pixel of the background has value 0 and for the pixels of the cells value >0. Pixels of the same object (cell) have the same label value.

[nkeim]

Thanks. It sounds like you can use skimage.measure.regionprops() to get the centroids of the labeled regions. See the trackpy bubble tracking tutorial for an example: http://soft-matter.github.io/trackpy/v0.5.0/tutorial/custom-feature-detection.html

[Ciro1990]

Thanks a lot! It works now :)