pyimgal 0.1.0

Python wrapper and bindings for imgal.

pyimgal

The pyimgal package serves as the Python bindings wrapper for imgal.

Installation

pyimgal from PyPI

You can install pyimgal from PyPI with:

pip install pyimgal

imgal_python from source

To build the pyimgal Python bindings from source, use the maturin build tool. If you're using uv you can do the following in the imgal_python crate directory to build the Python bindings:

$ cd imgal_python
$ uv run maturin develop --release

This will create a .venv in the local directory, compile the imgal Rust library and the imgal_python PyO3 bindings and install the bindings in the venv as pyimgal.

Alternatively if you're using conda or mamba you can do the following:

$ cd imgal_python
$ mamba activate myenv
(myenv) $ mamba install maturin
...
(myenv) $ maturin develop --release

Using imgal with Python

Once pyimgal has been installed in a compatiable Python environment, imgal will be available to import. The example below demonstrates how to obtain a colocalization z-score (i.e. colocalization and anti-colocalization strength) using the Spatially Adaptive Colocalization Analysis (SACA) framework. The two number values after the channels are threshold values for channels a and b respectively.

import imgal.colocalization as coloc
from tifffile import imread

# load some data
image = imread("path/to/data.tif")

# slice channels to perform colocalization analysis
ch_a = image[:, :, 0]
ch_b = image[:, :, 1]

# perform SACA 2D
coloc_zscore = coloc.saca_2d(ch_a, ch_b, 500.0, 500.0)