remove_background#

This script removes the stationary background of a tif sequence in a given folder. Specifically, it does:

  • Median z-projection

  • divide raw images by the projection

By default, it replaces the original images with background removed images.

Syntax

python remove_background.py img_folder

  • img_folder – A folder of tiffstacks.

Note

Here the processed images are converted to 8-bit images. Autocontrast is applied.

Warning

Since the bifurcation images always require background subtraction, this procedure is included in the “crop_channel.py” script. We can still apply this script, but it essentially has no effect.

Edit

  • Nov 03, 2022 – Initial commit.

  • Jan 04, 2023 – (i) Target on a folder of tiffstacks. Remove the background of each tiffstack, based on their own median image. (ii) Change default saving behavior: now REPLACE the original images with background removed images.

  • Jan 05, 2023 – Adapt myimagelib import style.

  • Feb 08, 2023 – Rewrite in function wrapper form, to make autodoc work properly. (autodoc import the script and execute it, so anything outside if __name__=="__main__" will be executed, causing problems)