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Manual installation

This guide covers manual installation using conda, pip, and uv for users who prefer a command-line setup or are developing SenoQuant.

Note: For most users, the installers are recommended as they simplify setup and ensure GPU support.

Create an environment

In your terminal (Command Prompt/PowerShell on Windows, Terminal on macOS/Linux), create and activate a new conda environment with Python 3.11.

conda create -n senoquant python=3.11
conda activate senoquant

You should see (senoquant) at the beginning of your terminal prompt, indicating that the environment is active.

Install uv and napari

We strongly recommend using uv instead of pip because standard pip often has difficulty solving complex dependencies. uv is also much faster.

pip install uv
uv pip install pip-system-certs
uv pip install "napari[all]"

Note: pip-system-certs enables Python to use your system's certificate store for SSL verification. This helps avoid certificate errors when downloading packages or models, especially on corporate networks or systems with custom certificate authorities.

Alternatively, using standard pip:

pip install "napari[all]"

Install SenoQuant

uv pip install senoquant

Alternatively, using standard pip (not recommended. This might be fine for napari, but often fails for SenoQuant):

pip install senoquant

Warning (Windows): Installing via pip/uv may not pull a GPU-enabled PyTorch build on Windows. If you need GPU acceleration, use the Windows installer instead. Or, troubleshoot PyTorch installation manually by following the official PyTorch instructions.

BioFormats (Java) setup

SenoQuant uses format-specific BioIO readers (for example bioio-czi, bioio-ome-tiff, and bioio-ome-zarr) for fast data loading and uses BioFormats via bioio-bioformats for metadata extraction when available. BioFormats requires Java, which is automatically installed as a dependency of SenoQuant.

If you get a JVMNotFoundException when reading images, set JAVA_HOME manually:

  • macOS/Linux: export JAVA_HOME=$CONDA_PREFIX
  • Windows: set JAVA_HOME=%CONDA_PREFIX%\Library

Optional dependencies

  • uv pip install senoquant[all] for full stack.

Launch

Start napari from your terminal:

napari --with senoquant

The first launch of napari and the SenoQuant plugin will be slower as napari initializes and SenoQuant downloads model files (a few GBs) from Hugging Face. Subsequent launches will be faster as models are cached locally.

Make sure the terminal remains open while using napari to keep it running. The terminal also displays useful info/warning/error messages.

Development installation

For development work, install SenoQuant from the repository in editable mode:

pip install uv
uv pip install -e .

This allows you to make changes to the code and see them reflected immediately without reinstalling.