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This is a scratch repo for the OME-NGFF Hackathon Zurich 2024

required cellpose version: 2.2.1

Input:

Shape: (279, 2, 91, 554, 928)

Size: ~50 gb

Example for otsu segmentation:

n_workers = 4

threads_per_worker = 1

region_shape = (1, 1, 91, 554, 928)

Output chunks: (1, 1, 48, 128, 128)

Read-process-write took roughly 4-5 min.

Example output for cellpose segmentation:

Shape: (279, 2, 91, 317, 325)

Size: ~10 gb