Napari plugin for segment anything version 2 model from meta. Plugin primarily useful for segmenting 3d volumetric data or 3d time series data.
Project description
napari-SAMV2
Napari plugin to use segment anything version 2 models from Meta.
Plugin primarily made for segmenting 3d volumetric data or 3d time series data.
Installation
You can install napari-SAMV2
via pip:
pip install napari-SAMV2
Pre-requisite of samv2 installation needed:
git clone https://github.com/facebookresearch/segment-anything-2.git
cd segment-anything-2
pip install -e .
The plugin and installation tested with python 3.10 in conda environment with pytorch-cuda=12.1
If you are installing samv2 in a separate environment, you can follow the below tested env,
conda create -n samv2_env python=3.10
conda activate samv2_env
conda install pytorch torchvision torchaudio pytorch-cuda=12.1 -c pytorch -c nvidia
python -m pip install "napari[all]"
git clone https://github.com/facebookresearch/segment-anything-2.git
cd segment-anything-2
pip install -e .
pip install napari-SAMV2
To install latest development version :
pip install git+https://github.com/Krishvraman/napari-SAMV2.git
Usage
Middle mouse click - positive point
Ctrl + Middle mouse click - negative point
Time Series Segmentation :
Volume Segmentation :
Reference :
Example Data from in demo videos from, Cell tracking challenge - https://celltrackingchallenge.net/ 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.
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