segment_cells_3d
Segment cells in 3D volumes using Cellpose, with options for full 3D or slice stitching, adjustable diameter, and GPU acceleration.
Instructions
Segment cells in a 3D volume using Cellpose.
Args: image_path: Path to input 3D image stack (TIFF, etc.) model_type: Cellpose model type diameter: Expected cell diameter in pixels do_3d: Use full 3D segmentation (True) or slice + stitch (False) anisotropy: Z-axis anisotropy factor (z_pixel_size / xy_pixel_size) stitch_threshold: Threshold for stitching masks across slices (if do_3d=False) flow3d_smooth: Smoothing factor for 3D flows channels: Channel specification [cyto, nuclei] or None gpu: Whether to use GPU acceleration output_path: Optional path to save masks
Returns
Dictionary with 3D segmentation resultsInput Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gpu | No | ||
| do_3d | No | ||
| channels | No | ||
| diameter | No | ||
| anisotropy | No | ||
| image_path | Yes | ||
| model_type | No | cyto3 | |
| output_path | No | ||
| flow3d_smooth | No | ||
| stitch_threshold | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||