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.

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.