bioimage 0.1.3

bioimage - library to make working with biomedical images more comfortable

bioimage

Library for convenient handling of bioimages

Contains the following modules:

io

Convenient file management, uses pims and pycomfort under the hood. For example:

• load_bio_image(from_file: Path) that allows loading microscopy images
• load_frame(from_file: Path): that loads first frame of the microscopy image from the system path

filters

Useful filters to process images. For example:

• rolling ball filter to fix some issues on the background
• local_contrast filter that can be used together with thresholding to find boundaries of the objects
• gray2color that deals with fluorescent images
• glowing - for dealing with comparisons between normal and fluorescent images

comparisons

When you need to compare multiple conditions For example:

• show_images that displays images from the whole folder as a grid plot
• folder_to_conditions that allows splitting images in the folder to multiple conditions based on their namings
• get_glowing_overlays that allows combining fluorescent and phase-contrast images