GallowayLabMIT / rushd

Package for maintaining robust, reproducible data management
MIT License
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Add image processing + scale/scalebar extraction #16

Open meson800 opened 10 months ago

meson800 commented 10 months ago

Let's actually add some of the image processing code to rushd! Ideally we want:

  1. Some simple linear image processing, such as loading scale bars, black balance, other linear scalings, recoloring, etc.
  2. Layout functions that create a grid of plots, with axis labels.

Of note, PIL still does not support (python-pillow/Pillow#1888) high bit rate images. This means we should probably use tifffile to do the loading to numpy arrays directly, so we don't lose high-bit rate images (either from the Keyence or other sources).

To load the Keyence metadata, the Keyence appends XML metadata to the end of tiff's it generates. We can read this, and match it up with the harcoded scale values to automatically detect capture metadata and be able to generate scale bars at a certain resolution.

kaseylove commented 1 month ago

Extract Nikon & Keyence metadata from images