Image cleaner module

This module takes clear of cleaning up the junk from outside the brain area by using masks.

class library.image_manipulation.image_cleaner.ImageCleaner

Bases: object

Methods for cleaning images [and rotation, if necessary]. ‘Cleaning’ means applying user-verified masks (QC step) to downsampled or full-resolution images

create_cleaned_images()

This method applies the image masks that has been edited by the user to extract the tissue image from the surrounding debris

create_cleaned_images_full_resolution(channel=1)

Clean the image using the masks for the full resolution image

create_cleaned_images_thumbnail(channel=1)

Clean the image using the masks for the downsampled version

parallel_create_cleaned(INPUT, CLEANED, MASKS)

Do the image cleaning in parallel

Parameters:

  • INPUT – str of file location input

  • CLEANED – str of file location output

  • MASKS – str of file location of masks