Read and manipulate cs files


in the 3D Variability analysis tutorial video you mention that there is a simple way to read and manipulate cs files such that the content could be plotted elsewhere. @apunjani in the video mentioned that there is a tutorial on this available. Sadly I was not able to find this. I only found that there are details forthcoming in the data management tutorial. Could you give a rough intro in how this is achieved?

Thank you and Best,


This is all I can find right now, a detailed tutorial would be very helpful:

Thanks @olibclarke , yes this I also found but it is hardly specific enough to be useful.

Did anyone manage to read the file somehow?

They are just numpy structured arrays (recarrays). It’s easy to do whatever you want in an ipython session or notebook.

import numpy as np
cs = np.load("file.cs")

thanks a lot! This works.

Cool. Make sure cs['uid'] always agrees between any particle sets you are comparing!

(If you have pyem, you can also use pyem.metadata and libraries for relational operations, correlating to Relion, cisTEM/FREALIGN, etc.)

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Hi @david.haselbach, @olibclarke,

Please see our new tutorial on reading and manipulating .cs files!


Hi @stephan,

this looks great I am looking forward to trying. Thanks a lot!



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