Hello. I am trying to write a script to analyze particles after 2D classification. Does the ‘alignments2D/shift’ field represent the number of pixels, with the pixel size being the pixel size of the extracted particles? I really appreciate your help!


Yeah, that’s right. You can follow the conversion code in pyem.metadata.cryosparc2 if you want to see.

Thank you so much, Daniel! Always so helpful :slight_smile:

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Just a minor clarification – the alignments{2D,3D}/shift gives the shift in pixels where the pixel size is given by the alignments{2D,3D}/psize_A field. Multiplying them will give the shift in Angstroms