Segmentation workflow with napari-assistant

Please keep in mind that Convpaint’s aim and functionalities are limited to pixel prediction, which is usually just a first step in a segmentation workflow. Fortunately, the napari ecosystem is very powerful and flexible.

In the following example we use napari-convpaint as a first step for pixel prediction and complete the segmentation using tools bundlend in the napari-assistant plugin (developed by Robert Haase).

You can see the complete workflow in the video below:

Installing napari-segment-blobs-and-thing-with-membranes

If you want to replicate the workflow shown in the video, you need to install the napari-segment-blobs-and-things-with-membranes plugin.

To achieve this, you can open napari and navigate to the Plugins menu. In the “Install/Uninstall Plugins…” section you can then use the search menu to find napari-segment-blobs-and-things-with-membranes.

Press the install button to add it to your napari plugins.

For more information about that plugin and other ways of installing it please refer to its docs.