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MunskyGroup / FISH_Processing

Repository to automatically process ​Fluorescence In Situ Hybridization (FISH) images using Cellpose and BIG-FISH (FISH-quant v2).
BSD 3-Clause "New" or "Revised" License
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BigFISH Spot Decomposition mixup #4

Open ericron opened 2 months ago

ericron commented 2 months ago

For the Spot detection there is a mix up of the inputs for voxel_size and object_radius.

The code should have psf values in nanometers define the voxel_size_nm and the object_radius_nm is the approximate size of the mRNA spot in nanometers.

There are also hard coded parameters for cluster decomposition (alpha, betta, gamma, and cluster_radius) that dramatically change the spot counts when changed.

luisub commented 2 months ago

Hi @ericron I added you as administrator of the repository. Please add and push the changes needed.