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Installation guide ⚙

This guide outlines the steps for installing CellSeg3D and its dependencies. The plugin is compatible with Windows, Linux, and MacOS.

Note for ARM64 Mac Users: Please refer to the :ref:`section below <source/guides/installation_guide:ARM64 Mac installation>` for specific instructions.

Warning

If you encounter any issues during installation, feel free to open an issue on our GitHub repository.

Installing pre-requisites

PyQt5 or PySide2

CellSeg3D requires either PyQt5 or PySide2 as a Qt backend for napari. If you don't have a Qt backend installed:

pip install napari[all]

This command installs PyQt5 by default.

PyTorch

For PyTorch installation, refer to PyTorch's website , with or without CUDA according to your hardware. Select the installation criteria that match your OS and hardware (GPU or CPU).

Note

While a CUDA-capable GPU is not mandatory, it is highly recommended for both training and inference.

  • Running into MONAI-related errors? Consult MONAI’s optional dependencies for solutions. Please see MONAI's optional dependencies page for instructions on getting the readers required by your images.

Installing CellSeg3D

Via pip:

pip install napari-cellseg3d

Directly in napari:

  • Navigate to Plugins > Install/Uninstall Packages
  • Search for napari-cellseg3d

For local installation (after cloning from GitHub) Navigate to the cloned CellSeg3D folder and run:

pip install -e .

Successful installation will add the napari-cellseg3D plugin to napari’s Plugins section.

ARM64 Mac installation

For ARM64 Macs, we recommend using our custom CONDA environment. This is particularly important for ARM64 (Silicon chips) MacBooks.

Start by installing miniconda3.

Creating the environment

  1. Clone the repository (link):
git clone https://github.com/AdaptiveMotorControlLab/CellSeg3d.git

2. Create the Conda Environment : In the terminal, navigate to the CellSeg3D folder:

cd CellSeg3D
conda env create -f conda/napari_cellseg3d_ARM64.yml

This will also install the necessary dependencies as well as the plugin.

  1. Activate the environment :
conda activate napari_cellseg3d_ARM64

4. Install a Qt backend : Important : you only need to install one of the following backends. PyQt5:

pip install PyQt5

OR PySide2:

pip install PySide2

5. Install PyTorch : Refer to PyTorch's website for installation instructions.

6. Launch napari : You should now see the CellSeg3D plugin in the Plugins section of napari. See Usage section for a guide on how to use the plugin.

Updating the environment

In order to update the environment, navigate to the CellSeg3D folder and run:

conda deactivate
conda env update -f conda/napari_cellseg3d_ARM64.yml

Optional requirements

Additional functionalities

Several additional functionalities are available optionally. To install them, use the following commands:

  • CRF post-processing:
pip install pydensecrf@git+https://github.com/lucasb-eyer/pydensecrf.git#egg=master
  • Weights & Biases integration:
pip install napari-cellseg3D[wandb]
  • ONNX model support (EXPERIMENTAL): Depending on your hardware, you can install the CPU or GPU version of ONNX.
pip install napari-cellseg3D[onnx-cpu]
pip install napari-cellseg3D[onnx-gpu]

Development requirements

  • Building the documentation:
pip install napari-cellseg3D[docs]
  • Running tests locally:
pip install pydensecrf@git+https://github.com/lucasb-eyer/pydensecrf.git#egg=master
pip install napari-cellseg3D[test]
  • Dev utilities:
pip install napari-cellseg3D[dev]