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Helper function for scaling images #415
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Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
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Only aesthetic comments
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Looks pretty good, just a few suggestions on taking advantage of numpy
's duck array for xarray
s along with a small testing question.
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Looks good! Just a single failing test fix.
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Looks good, just one small comment
Will you send me the TIFs at different downsampling ratios? |
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I would add the downscaling coefficient as an argument that gets defaulted to 0.25 for the places where it's called in the notebooks, rather than a hidden variable.
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What is the purpose of this PR?
Closes #403. Adds a helper function that changes resolution of image data by scaling the size of the FOV.
Implement this function in notebook 3f to change resolution of FOVs to match the rest in the run
How did you implement your changes
Use
skimage.transform.rescale()
to scale the data in the helper functionrescale_image()
.Remaining issues
Implement this helper function in:
stitch_images()
Here is an exampled of downscaled rosetta stitched images. Both the 0.5 and 0.25 images can now be opened in fiji, and the default is currently set to 0.25.
Original stitched image: (69632 x 10240)
Downscaled by 0.5: (34816 x 5120)
Downscaled by 0.25: (17408 x 2560)