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Add code for cryo lamella segmentation #116

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Add code for cryo lamella segmentation #116

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2 changes: 2 additions & 0 deletions scripts/cryo/lamella/.gitignore
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Original file line number Diff line number Diff line change
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embeddings/
segmentations/
19 changes: 19 additions & 0 deletions scripts/cryo/lamella/mito_segmentation_micro_sam.py
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from micro_sam.sam_annotator import image_folder_annotator

ROOT = "/home/pape/Work/data/fernandez-busnadiego/lamella/Filtered_lamellae"


def main():
tile_shape = (384, 384)
halo = (64, 64)
image_folder_annotator(
ROOT, "./segmentations",
model_type="vit_b_lm", embedding_path="./embeddings",
tile_shape=tile_shape, halo=halo,
precompute_amg_state=True,
skip_segmented=False,
)


if __name__ == "__main__":
main()