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Installation

Easy Way!

To install this plugin you need to use mamba or conda to create a environment and install the requirements. Use commands below to create the environment and install the plugin: 

git clone https://github.com/juglab/featureforest
cd ./featureforest

# for GPU
mamba env create -f ./env_gpu.yml

# if you don't have a GPU
mamba env create -f ./env_cpu.yml

Note

You need to install sam-2 which can be installed easily using mamba (or conda). To install sam-2 using pip please refer to the official sam-2 repository.

Requirements

  • python >= 3.10
  • numpy==1.24.4
  • opencv-python
  • scikit-learn
  • scikit-image
  • matplotlib
  • pyqt
  • magicgui
  • qtpy
  • napari
  • h5py
  • pytorch=2.3.1
  • torchvision=0.18.1
  • timm=1.0.9
  • pynrrd
  • segment-anything
  • sam-2

Installing Only The Plugin

If you use the provided conda environment yaml files, the plugin will be installed automatically. But in case you already have the environment setup, you can just install the plugin. First clone the repository: 

git clone https://github.com/juglab/featureforest
Then run the following commands: 
cd ./featureforest
pip install .

There is also a pypi package available that you can install using pip: 

pip install featureforest

If you want to install the plugin manually using GPU, please follow the pytorch installation instruction here. For detailed napari installation see here.