Running plugin

You can drag and drop a variety of images into napari. You can also open a folder of images to process together (or sequentially). See napari image documentation for more advanced image loading.

2D images

Here is an example of the plugin running on the 2D sample image.

3D_demo

Batch processing in 2D

Cellpose will process all images in an opened folder with the same settings and return masks for each image with the name folder_name_fileid. You can export all the images in the napari File menu.

Here is an example of the plugin running on a folder of 2D data.

time_series_demo

3D segmentation

Cellpose can segment 3D and 4D stacks. If there is a channel axis, specify it by labelling it with ‘c’.

To run 3D processing, check process stack as 3D.

If the 3D segmentation is not working well and there is inhomogeneity in Z, try stitching masks using the stitch threshold slices option instead of checking process stack as 3D. In this setting, cellpose will create masks in 2D on each XY slice and then stitch them across slices if the IoU between the mask on the current slice and the next slice is greater than or equal to the stitch threshold slices.

Here is an example of the plugin running on the 3D sample image.

3D_demo

Time segmentation

Stitching can also be applied in time by setting stitch threshold slices>0.

Here is an example of the plugin running on cell tracking challenge data.

time_series_demo