Allen Cell Discussion Forum

Separating zstacks into individual cells

I saw that you used .npz files in the notebook on cell shape analysis. How can I go from, say segmenting fibrous actin(same workflow as tight junction protein) to separating each individual cell ?

The cell shape analysis jupyter notebook is developed by our modeling team, not directly integrated with segmenter. I would suggest you to take a look at this jupyter notebook: https://github.com/AllenInstitute/aics-segmentation/blob/master/lookup_table_demo/bridging_the_gap_between_binary_image_and_analysis.ipynb

It does exactly what you need, providing two ways to go from segmentation to individual “objects”.

Thanks,
Jianxu

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That’s what I was hoping to find! Thanks!
The function returns the labelled pixels/voxels. While it does not seem to save them separately, I was able to find out a way to separate the objects into individual files.

Thanks,
Pushkar