Generating Nuclei Segmentations for vEM datasets using Cellpose v1

This protocol details the process of generating nucleus segmentations in FIB-SEM (Focused Ion Beam Scanning Electron Microscopy) image stacks of cells and tissues using Cellpose. These segmentations are crucial for gaining biological insights and training deep learning models on cell and organelle segmentation. The protocol covers the application of Cellpose for fine-tuning 2D models specifically for nuclei segmentation. Once fine-tuned, the model is used to generate 3D predictions for the entire dataset. These segmentations can be further refined through manual approaches, utilized for visualization, or employed in training other machine learning models.