Examples for using the micro_sam annotation tools:
annotator_2d_wsi.py: Run the interactive 2d annotation tool, suitable for whole-slide images (WSIs).annotator_2d.py: Run the interactive 2d annotation tool.train_pannuke_semantic.py: Train a model for semantic segmentation of nuclei in PanNuke histopathology images.
There are Jupyter Notebooks available for using automatic segmentation and finetuning on some example data in the notebooks folder located in the micro-sam repository.
The folder finetuning contains example scripts that show how a Segment Anything model can be fine-tuned on custom data with the micro_sam.train library, and how the finetuned models can then be used within the micro_sam annotation tools.