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vanvalenlab / deepcell-tf

Deep Learning Library for Single Cell Analysis
https://deepcell.readthedocs.io
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Segmentation Mask Output #703

Closed tbudiman7 closed 9 months ago

tbudiman7 commented 9 months ago

Hi VanValen Lab,

We have successfully generated segmentation masks using Mesmer and when we opened them on Fiji, the masks look like cell outlines. However, this is causing problems in our downstream analysis which were never a problem when we used segmentation masks generated by Ilastik and CellProfiler. I have attached images of both segmentation masks below, the one generated by Ilastik is filed in whereas the one on Mesmer is not. Is there a way to generate masks with filed holes?

Thank you.

Mesmer seg mask Ilastik seg mask

rossbar commented 9 months ago

The masks produced by mesmer is a label image, i.e. where each pixel that corresponds to an instance of an individual cell is assigned a value corresponding to the index of the cell. In other words, the masks from mesmer are "filled in" - the fact that you're only seeing mask outlines likely has something to do with how Fiji is configured to load data.