Installation

OMIO targets Python 3.12 and higher and builds on the standard scientific Python stack commonly used in microscopy and large scale image processing workflows. Core dependencies include NumPy, tifffile, zarr, dask, napari, and related libraries for metadata handling and image I/O.

Recommended installation method

The recommended way to install OMIO for end users is via the Python Package Index (PyPI):

conda create -n omio python=3.12 -y
conda activate omio
pip install omio-microscopy

For developers

For development work or reproducible analysis pipelines, it is often convenient to install OMIO from source:

git clone https://github.com/FabrizioMusacchio/OMIO.git
cd OMIO
pip install .

Alternatively, OMIO can be installed directly from GitHub without cloning the repository:

pip install git+https://github.com/FabrizioMusacchio/OMIO.git

If you plan to modify the code, use an editable installation:

pip install -e .

or, to include development dependencies such as testing and documentation tools:

pip install -e .[dev]

Avoid mixing local source folders and installed packages with the same name in the same working directory, as this can lead to confusing import behavior and unexpected imports during development.

Upgrading OMIO

To upgrade OMIO to the latest version from PyPI, use:

pip install --upgrade omio-microscopy

In case you have installed OMIO from source, you can upgrade to the latest version from GitHub with:

pip install --upgrade git+https://github.com/FabrizioMusacchio/OMIO.git

or, if you have downloaded the source code, by running the following command in the source directory:

pip install --upgrade .[dev]