napari-SAMV2 0.0.3

Napari plugin for segment anything version 2 model from meta. Plugin primarily useful for segmenting 3d volumetric data or 3d time series data.

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.

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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 .

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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    

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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

Example Data from :

Cell tracking challenge - https://celltrackingchallenge.net/

FlyEM project - https://www.janelia.org/project-team/flyem/hemibrain

Time Series Segmentation :

https://github.com/user-attachments/assets/610ce965-bb97-453f-8fff-c5de5f14162c

Volume Segmentation :

https://github.com/user-attachments/assets/adb409be-c3ba-4f03-ac0a-ceb2da0c0c83

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.