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
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