Napari plugin to use segment anything version 2.1 models from Meta.
Plugin made for segmenting 3d volumetric data or 3d time series data.
The plugin requires the following pre-requisite to be installed :
- Python and pytorch versions
python>=3.10,torch>=2.5.1 and torchvision>=0.20.1 required
To install pytorch with your respective OS please visit - https://pytorch.org/get-started/locally/
- SAM v2 installation from meta
Please refer https://github.com/facebookresearch/sam2
- Install napari
python -m pip install "napari[all]"
Following is a sample conda environment installation with the above pre-req
conda create -n samv2_env python=3.10
conda activate samv2_env
pip3 install torch torchvision
git clone https://github.com/facebookresearch/sam2.git && cd sam2
pip install -e .
python -m pip install "napari[all]"
pip install napari-SAMV2
Middle mouse click - positive point or keyboard shortcut "a"
Ctrl + Middle mouse click - negative point or keyboard shortcut "n"
Time Series Segmentation :
Volume Segmentation :
Reference :
Example Data in the demo videos are from,
Cell tracking challenge - https://celltrackingchallenge.net/
and
FlyEM project - https://www.janelia.org/project-team/flyem/hemibrain
Distributed under the terms of the BSD-3 license, "napari-SAMV2" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.