Re: [scipion-users] 2D classification in streaming

[Genís V. G. <gen...@ki...>]

Hi everyone and thanks for all the replies!

The three suggested approaches allowed me to automatically separate good from bad 2D classes.

"cryoassess", "xmipp-eliminate empty classes" and "gl2d" produce a SetOfAverages or a SetOfClasses2D.

I know I can use a SetOfAverages as an input to xmipp-ransac or eman2-initial model. However, is it possible to use these to generate an initial model with relion or cryosparc?

Best regards


Genis Valentin Gese | Postdoctoral researcher

Martin Hällberg group
Cell and Molecular Biology Department | Karolinska Institutet
171 65 Stockholm | Solnavägen 9
gen...@ki...<mailto:fir...@ki...> | ki.se<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fki.se%2Fen%2Fstartpage&data=02%7C01%7Cgenis.valentin.gese%40ki.se%7C96f824255829424948f308d82a5e4ec9%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637305931833981292&sdata=yXbUoiFkJqjlBIYtLNaNEXIlydBY8N0LVZ5C9bWR5nU%3D&reserved=0>

________________________________
Från: Carlos Oscar Sorzano <co...@cn...>
Skickat: den 10 maj 2021 09:39
Till: Mailing list for Scipion users <sci...@li...>; Genís Valentín Gesé <gen...@ki...>
Ämne: Re: [scipion-users] 2D classification in streaming


Dear Genis,


the idea is that cryoassess is used as a static protocol, labels the class representatives into good and bad classes, and then GL2D classifies in streaming all the particles into these classes.


Cheers, Carlos Oscar


El 09/05/2021 a las 11:15, Genís Valentín Gesé escribió:
Hello all!

At the moment I'm using "xmipp-gl2d static" to classify a streaming set of particles, and it would be great if one could get a stream of particles belonging to the good 2d classes.

In this way, one could use 2D classification to filter out bad particles before further processing.

I looked into cryoasses, but it does not seem to run in streaming mode.

Any ideas on whether this can be done?

Thanks and best regards


Genis Valentin Gese | Postdoctoral researcher

Martin Hällberg group
Cell and Molecular Biology Department | Karolinska Institutet
171 65 Stockholm | Solnavägen 9
gen...@ki...<mailto:fir...@ki...> | ki.se<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fki.se%2Fen%2Fstartpage&data=04%7C01%7Cgenis.valentin.gese%40ki.se%7C9537b354fd5743ec20f808d913978e43%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637562363919527485%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=hwzBc77vMs%2F%2FBrwyainuJus8R10IIjI2ABz1EaCShQc%3D&reserved=0>




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