Installation

Requirements

Twocan requires Python 3.8 or later and has the following dependencies:

• numpy

• pandas

• opencv-python

• scikit-image

• scikit-learn

• spatialdata

• optuna

• tifffile

Installing from Source

# Clone the repository
git clone https://github.com/camlab-bioml/twocan.git
cd twocan

# Create and activate conda environment
conda env create -f environment.yml
conda activate twocan

# Install the package
pip install .

Installing from PyPI

Note

PyPI installation will be available in future releases.

pip install twocan

Development Installation

For development, install in editable mode with development dependencies:

# Clone and enter directory
git clone https://github.com/camlab-bioml/twocan.git
cd twocan

# Create conda environment
conda env create -f environment.yml
conda activate twocan

# Install in development mode
pip install -e .

# Install additional development dependencies
pip install pytest sphinx nbsphinx myst-nb sphinx-rtd-theme

Verification

To verify your installation, run:

import twocan
print(twocan.__version__)

# Test basic functionality
from twocan import RegEstimator, IFProcessor, IMCProcessor
print("Twocan installed successfully!")