DL in napari

DL in napari#

Some DL in napari plugins#

Stardist#

For a comprehensive overview of stardist in napari check out this workshop tutorial

Cellpose#

A 2D cell segmentation with cellpose shown in napari

From Carsen Stringer’s group at HHMI Janelia Research Campus.

For more info see here.

Steps:

  1. File > Open Sample > cellpose-napari > Cells 2D

  2. Plugins > cellpose

  3. Check cellpose options in screenshot to repeat

# !pip install git+https://github.com/MouseLand/cellpose-napari

Segment anything#

Screenshot of cells being segmented with napari segment anything plugin

From Jordão Bragantini of the Royer lab, CZ Biohub

For more info see here

# !pip install git+https://github.com/royerlab/napari-segment-anything.git@fix-napari-colors

napari-convpaint#

napari-convpaint for interactive segmentation

napari-convpaint by Guillaume Witz for interactive segmentation using pretained NN models.

# !pip install git+https://github.com/guiwitz/napari-convpaint.git

CellCanvas#

A screenshot of cellcanvas interactive segmentation tool

CellCanvas is a tool made by Kyle Harrington and Kevin Yamauchi along with more collaborators like Lorenz Lamm, Kevin Zhao, and Utz Ermel.

Example data

# !pip install git+https://github.com/cellcanvas/cellcanvas.git@dl-at-mbl-2024

import napari

viewer = napari.Viewer()
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