Cellpose

Parser for Cellpose segmentation results.

Refer to API: CellposeSegmentation

Example of loading cellpose segmentation results

from neuralib.cellpose import read_cellpose

# Load cellpose segmentation result (.npy file)
seg = read_cellpose("/path/to/cellpose_seg.npy")

# Get number of segmented cells
print(f"Number of cells: {seg.n_segmentation}")

# Get image dimensions
print(f"Image size: {seg.width} x {seg.height}")

# Access segmentation masks (0 = background, 1,2,... = cell labels)
masks = seg.masks  # Array[uint16, [H, W]]

# Access cell outlines
outlines = seg.outlines  # Array[uint16, [H, W]]

# Get cell center coordinates
centers = seg.points  # Array[int, [N, 2]]

# Get cell diameter used in segmentation
print(f"Cell diameter: {seg.diameter}")

Convert to ImageJ ROI

from neuralib.cellpose import cellpose_point_roi_helper

# Convert segmentation to ImageJ point ROI
cellpose_point_roi_helper(
    "/path/to/cellpose_seg.npy",
    "/path/to/output.roi"
)