Segment Anything V2

Napari plugin to use segment anything version 2.1 models from Meta.

Plugin made for segmenting 3d volumetric data or 3d time series data.

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Installation¶

The plugin requires the following pre-requisite to be installed :

1. 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/

2. SAM v2 installation from meta

Please refer https://github.com/facebookresearch/sam2

3. 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

Usage¶

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

License¶

Distributed under the terms of the BSD-3 license, "napari-SAMV2" is free and open source software

Issues¶

If you encounter any problems, please file an issue along with a detailed description.