Segmentation of mammary gland cells

VollSeg specializes with its seed pooling approach to segment irregular shapes of mammary gland cells

from human or mouse samples. In the orignal algorithm we use a CARE trained denoising model and either use the U-Net model for semantic segmentation or use a denoising model for the semantic segmentation depending on which model has a better prediction. Denoising model is used to denoise the image first and the result is then passed to the segmentation models. For using combination of (U-Net, CARE and StarDist) model with U-Net as the model for semantic segmentation use this script if you want to use the denoised image as the base image for creating the semantic segmentation map using Otsu threshold set the parameter dounet=False in that same script.