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spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
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Are the masks in the left in the tutorial really two cells? #1926

Closed vals closed 3 years ago

vals commented 3 years ago

[ Related to openjournals/joss-reviews/issues/2440 ]

Are the masks in the left of the example in the tutorial two cells? There seems to be two nuclei, but are they two cells? Maybe a different less confusing FOV could be used? Or this could be commented upon in the segmentation section of the Quick Start tutorial.

image

neuromusic commented 3 years ago

Indeed, they are!

As noted in the quick-start, the cells in this dataset express either the mouse or human ACTB gene, but not both. This can be seen by exploring each of the images in the stack, where you can see that, despite the apparent ambiguity, the segmentation has distinguished between two cells... one expressing the human ACTB and one expressing the mouse ACTB.

neuromusic commented 3 years ago

I've added a clarification to the quickstart.