organelles sub-module
The code in this sub-module have the routines to perform a (hopefully) robust inference of subcellular objects:
- 1️⃣-cellmask
- 2️⃣-nuclei
- 3️⃣-cytoplasm
- 4️⃣-lysosome
- 5️⃣-mitochondria
- 6️⃣-golgi
- 7️⃣-peroxisome
- 8️⃣-endoplasmic reticulum
- 9️⃣-lipid body
From the results of the 1️⃣-cellmask, 2️⃣-nuclei, the 3️⃣-cytoplasm, a mask of the cytoplasm for each cell of interest is derived.
By "inference of sub-cellular objects" we mean assigning each pixel to belonging to an organell as estimated from the florescence image in the apropriate channel. This is done here by image processing and thresholding.