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Re: [scipion-users] Export particles from cryosparc
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From: Pablo C. <pc...@cn...> - 2021-05-18 12:17:11
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Dear Dmitry, the import of CS metadata files (*.cs) is not supported in Scipion. Does CS has an option to export to star files. It rings a bell. On 18/5/21 9:53, Dmitry Semchonok wrote: > > Dear Grigory, > > The files are in mrc format. > > Please, let me try to explain more plan: > > I have a project in cryosparc. There I have cryosparc selected 2D > classes. I want to export the particles of those classes into SCIPION. > > So I I pressed Export (fig 1) and the program(cryosparc) created the > folder with mrc + other files (fig 2;3). I looked into J48 and found > many *.mrc files of the particles. But it is not 1 mrc = 1 particle. > It seems to be a mrc stuck - so I have several files inside 1 *.mrc > (fig 4) (you can also notice that they all have different sizes) > > So I need to export them somehow in SCIPION > > For that, I used the SCIPION export - images protocol where for the > files to add I put *.mrc. But the protocol seems to be added only 1 > mrc as 1 picture and instead of having 46392 particles I have ~600 > particles. > > (Also the geometry seems not preserved). > > So my question how to export the particles from cryosparc into SCIPION > correctly? > > Thank you! > > > > https://disk.yandex.com/d/Fv3Q1lpwEzSisg > <https://disk.yandex.com/d/Fv3Q1lpwEzSisg> > > > Sincerely, > > Dmitry > > > > >> On 17. May 2021, at 18:12, Grigory Sharov <sha...@gm... >> <mailto:sha...@gm...>> wrote: >> >> Hi Dmitry, >> >> mrc stacks should have "mrcs" extension. Is this the problem you are >> getting? >> >> Best regards, >> Grigory >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >> e-mail: gs...@mr... <mailto:gs...@mr...> >> >> >> On Mon, May 17, 2021 at 4:49 PM Dmitry Semchonok <Sem...@gm... >> <mailto:Sem...@gm...>> wrote: >> >> Dear colleagues, >> >> I would like to export the particles from cryosparc to SCIPION. >> >> How to do that? >> >> >> >> >> >> What I tried: >> >> >> 1.In cryosparc I pressed Export – to export the particles I am >> interested in. >> >> 2.In the folder Export – I found many mrc stacks with particles >> in each. >> >> 3.I tried to export them to SCIPION using Export particles but >> instead of reading each stack and combine them in the 1 dataset I >> received 1 particle / per each mrc stack. >> >> >> Any ideas? >> >> >> Thank you >> >> Sincerely, >> >> Dmitry >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
