How can I do 3D spot detection or 3D decoding?

spacetx / starfish

starfish: unified pipelines for image-based transcriptomics

https://spacetx-starfish.readthedocs.io/en/latest/

MIT License

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How can I do 3D spot detection or 3D decoding? #2010

Open hziyin opened 4 months ago

hziyin commented 4 months ago

Dear starfish developers, Firstly, thank you for creating such a useful tool for spot detection and decode analysis. It is said that the spot finding method "BlobDetector" can work in 3D and the spot decoding method "PerRoundMaxChannel" can work in 3D too. I am wondering if you can provide some examples for 3D spot finding and 3D decoding. It would be appreciated if you could tell more about how spot finding method works in 3D. Thanks for your help.

berl commented 4 months ago

hi @hziyin
the detection and decoding methods work should in 3D- here's the example of 3d spotfinding and decoding for smFISH data