Segmentation workflow#

This workshop takes you through the following topics with some hands on exercises:

This is a segmentation workflow:

  • Install PartSeg and napari-segment-blobs-and-things-with-membranes.
    Note: If you do not see PartSeg Widgets after installing PartSeg, close napari and reopen it.

  • Download the Sample Data and complete this lesson written by Kasia Kedziora.

    Note: The lesson lists a different version of napari (0.4.15) than the version you are using (0.4.17). However, the steps are the same.

    Note: The following parameter settings are referred to in the lesson by Kasia Kedsiora. They are listed here for your convenience.

    • PartSeg: ROI Mask Extraction parameters:

      • Median filtering (r = 2)

      • Thresholding ‘Otsu’

      • Opening (r = 5)

      • Fill holes (r = 100)

      • Size restriction (>400)

      • Connect by sides

      • Convex hull (r = 1)

    • Napari-segment-blobs-and-things-with-membranes: Gaussian Laplace filter

    • PartSeg: ROI analysis extraction parameters:

      • Mask (nuclei):

      • Manual Threshold (-2)

      • Size restriction (>3)

      • Connect by side

The final guide in this workshop is Jupyter notebooks and napari. It takes about 30 minutes to complete.