save_masks
Saves cell masks as tif, png, or npy, plus binary outlines and overlay images. Uses an existing mask file and optionally the original image for visualization.
Instructions
Save masks plus outlines and overlay visualizations.
Always writes three outputs: (1) masks in the chosen format, (2) outlines as a binary PNG, (3) overlay PNG (colored masks on image or black).
Args: mask_path: Path to existing mask file output_format: Output format for masks (tif, png, npy) output_path: Optional custom output path for the masks file image_path: Optional path to original image; if provided, overlay is drawn on it save_flows: Reserved for future use (flow fields not saved)
Returns
Dictionary with mask_path, outlines_path, overlay_path, and files_createdInput Schema
| Name | Required | Description | Default |
|---|---|---|---|
| mask_path | Yes | ||
| image_path | No | ||
| save_flows | No | ||
| output_path | No | ||
| output_format | No | tif |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||