Metadata-Version: 2.4
Name: pybioimage
Version: 0.1.0
Summary: A small package for custom image analysis tasks.
Author-email: Raphael Schleutker <raphaelschleutker@gmx.de>
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: scikit-image>=0.22.0
Requires-Dist: opencv-python>=4.6.0
Requires-Dist: numpy>=1.26.4
Requires-Dist: pandas>=2.2.1
Requires-Dist: pykuwahara>=0.3.2
Requires-Dist: black ; extra == "dev"
Requires-Dist: pytest>=8.3.4 ; extra == "test"
Provides-Extra: dev
Provides-Extra: test

# pybioimage

## Installation

To install ``pybioimage`` run the following command.

````
pip install pybioimage
````

## Usage

The package is divided into submodules for FRAP, vertex enrichment, and cell 
aggregation analysis. Each of these submodules exposes an ``Analyzer`` class,
which constitutes the main class to use. These classes are instantiated with a
path pointing to the respective image. In order to make 
that as simple as possible, there is a convenience function in the ``utils`` 
module called ``find_files()``. This function searches for and returns all 
files from a given path fulfilling certain requirements. You can use this to 
find all files that are supposed to be analyzed.

````python
from pybioimage.utils import find_files


# Find all TIFF files in the 'data' folder but ignores files and folders 
# starting with an underscore '_'. 
find_files("data", pattern=".*\\.tiff$", ignore="^_.*")
````

Using regular expression, you can further finetune which files to return and 
then use those to instantiate your analyzer.

