Export Segmentations

Parameters

Image layer: The napari image layer.

labels layer: The napari labels layer on which to the segmentations are located.

Export type:

• 2D images: Saves 2D segmentations (or label maps) in .tif files. (Use for single and batch mode segmentations)

• 3D image: Saves 3D segmentations (or label map) in a single .tif file.

Folder name: Name of the dataset directory to create. If the dataset folder already exists, the new data will be appended.

Save directory: Directory in which to save the segmentations. A subdirectory labeled masks will be created.

Export grayscale image: If checked, the grayscale (image layer) will be exported in the same export type selected and saved in a subdirectory labeled images.

Output

Creates or appends data to a directory with the folder name specified. The segmentations will then be saved in a subdirectory folder labeled masks.

Note

Selecting the export grayscale image option ensures the file structure is correct to use the dataset in the Finetune a model and Train a model modules. See a file structure example in the Training Best Practices section.