Installation
============

Install BactoScoop into a dedicated **Python 3.10** environment. Conda and uv
install the same package and dependencies. The public source repository is on
`GitHub <https://github.com/Bart-Steemans/bactoscoop>`_.

Install the latest stable release from
`PyPI <https://pypi.org/project/bactoscoop/>`_ using either environment option below.
This guide covers version **0.1.2**.

Conda
-----

In Anaconda Prompt or Anaconda PowerShell Prompt:

.. code-block:: powershell

   conda create -n bactoscoop python=3.10 pip -y
   conda activate bactoscoop
   pip install bactoscoop
   python -m pip check
   python -c "import bactoscoop; from importlib.metadata import version; print(version('bactoscoop'))"
   jupyter lab

uv
--

After installing `uv <https://docs.astral.sh/uv/getting-started/installation/>`_:

.. code-block:: powershell

   uv venv --python 3.10 .venv
   uv pip install --python .venv bactoscoop
   uv pip check --python .venv
   .\.venv\Scripts\python.exe -c "import bactoscoop; from importlib.metadata import version; print(version('bactoscoop'))"
   .\.venv\Scripts\jupyter.exe lab

uv downloads Python 3.10 when necessary. On macOS/Linux, use
``.venv/bin/python`` and ``.venv/bin/jupyter`` for the last two commands.

Choose a release or development source
--------------------------------------

The commands above install the latest stable release in a new environment.
To update an existing installation, run
``python -m pip install --upgrade bactoscoop`` or
``uv pip install --python .venv --upgrade bactoscoop``.
For reproducibility, pin this release with
``python -m pip install bactoscoop==0.1.2``.

To install the corresponding tagged GitHub release, run:

.. code-block:: powershell

   python -m pip install "bactoscoop @ git+https://github.com/Bart-Steemans/bactoscoop.git@v0.1.2"

For uv, replace ``python -m pip install`` with
``uv pip install --python .venv``. Check the
`latest GitHub release <https://github.com/Bart-Steemans/bactoscoop/releases/latest>`_
for newer tags. A development checkout uses an editable install:

.. code-block:: powershell

   git clone https://github.com/Bart-Steemans/bactoscoop.git
   cd bactoscoop
   python -m pip install -e .

Dependencies
------------

.. include:: ../generated/dependencies.rst

Omnipose is pinned to 1.0.6 and NumPy remains below 2. PyArrow supplies Parquet
export.

Open the examples
-----------------

Download and extract the
`release archive <https://github.com/Bart-Steemans/bactoscoop/archive/refs/tags/v0.1.2.zip>`_
for its TIFFs, masks, SVM models, and notebooks; those assets are separate from
the wheel. In JupyterLab, select the Python 3.10 analysis kernel and open a
walkthrough under ``examples/``. Its first cell copies the input dataset into
a fresh folder under ``~/bactoscoop_runs/``. Supplied masks are reused by default;
set ``RUN_SEGMENTATION=True`` to run fresh Omnipose inference.

See :doc:`quickstart` and the :doc:`../examples/three-channel` and
:doc:`../examples/five-channel` walkthroughs.