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haesleinhuepf / BioImageAnalysisNotebooks

Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more
https://haesleinhuepf.github.io/BioImageAnalysisNotebooks
BSD 3-Clause "New" or "Revised" License
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Spot detection quality control example notebook #23

Closed Shannon-E-Taylor closed 1 year ago

Shannon-E-Taylor commented 1 year ago

Hi,

I've finally gotten around to polishing an example notebook describing validating spot detection (from this thread https://forum.image.sc/t/valdiation-metrics-for-spot-detection/73335/7) - it's in the included notebook. I have also added an annotation file (cells3d_annotations.csv), the image itself was already in the repository.

Sorry this has taken so long - I had a major deadline then was on a (long and long overdue) holiday.

Hopefully this is useful? Let me know if there's anything I can add. I have some messier data that may be more realistic (lower quality spot detection and more ambiguous cells) if that is useful, but need to check if it's OK make publicly available.

Best, Shannon

haesleinhuepf commented 1 year ago

Awesome @Shannon-E-Taylor, thanks so much for this! I'll just merge your notebook and create a new chapter 'Algorithm validation' for it. We will later extend it for sure.

Thanks again!