Preprocessing: Crop stitching artefacts before Crop to ROI before Convert into 8-bit format throws error

Defense-Circuits-Lab / findmycells

An end-to-end bioimage analysis pipeline with state-of-the-art tools for non-coding experts

https://defense-circuits-lab.github.io/findmycells/

GNU General Public License v3.0

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Preprocessing: Crop stitching artefacts before Crop to ROI before Convert into 8-bit format throws error #11

Closed KonKob closed 1 year ago

KonKob commented 1 year ago

Preprocessing tested on test_data Strategies:

Crop stitching artefacts
Crop to ROI
Convert into 8-bit format

KonKob commented 1 year ago

The cropping indices specified in the ROIs correlate to the coordinates in the original image. Preprocessing with Crop stitching artefacts before Crop to ROIs can therefore produce errors. Probably because the preprocessed image has zero size. Switching the strategies to the following order does work:

Crop to ROIs
Crop stitching artefacts
Convert into 8-bit format Although combining Crop stitching artefacts and Crop to ROIs only makes sense, if your ROIs contain the borders of the images