[3dem] 3dem Digest, Vol 218, Issue 24

Fri Oct 17 12:24:12 PDT 2025

No clue why?

> On Oct 17, 2025, at 12:00 PM, 3dem-request at ncmir.ucsd.edu wrote:
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> Today's Topics:
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>   1. Re: Importing Particles from Cryosparc into Relion for
>      Processing (Daniel Asarnow)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 16 Oct 2025 19:43:09 -0700
> From: Daniel Asarnow <dasarnow at gmail.com>
> To: Lauren Pellows <Lauren.Pellows at colorado.edu>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Importing Particles from Cryosparc into Relion for
>    Processing
> Message-ID:
>    <CANBcHWpEdtN3qAemawAFyH2nDdDrTbh0PwAxNpTA177ObZuscQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Lauren,
> Thanks for using my software. What messages do you see from Relion? You
> must check both the run.out and run.err files for the extraction job - a
> major hint is any "particle outside micrograph" warning.
> 
> In all our image processing suites but one (nextPYP), particle extraction
> (using coordinates to duplicate the data around each particle into small
> images of uniform size) is a required preprocessing step for
> single-particle analysis jobs. It is up to you whether to import your new
> micrographs from Relion MotionCorr back into cryoSPARC, or to extract in
> relion. However, you will notice that the micrographs from Relion are
> upside-down relative to the ones from cryoSPARC, because Relion flips any
> .tif file when it is read into memory. Further, Relion and cryoSPARC also
> use opposite conventions for the Y origin. Further further again, cryoSPARC
> Import Particle jobs assume the Relion convention in the .star file - the
> coordinates are inverted. Thus csparc2star.py has several options to
> account for all use cases.
> 
> default : exported coordinates are inverted, so that the same micrographs
> can be used for extraction in Relion (as mentioned this was the only use
> case in the first versions of cryoSPARC)
> --inverty : exported coordinates are not inverted, so that if they are
> imported back into cryoSPARC, they will work, e.g. if you only run Class3D
> in Relion
> --flipy : no effect on coordinates, but flips CTF angles to account for the
> upside-down images (one can always run CTF estimation again instead)
> 
> I recommend you always inspect the pick locations on the micrographs either
> manually, with relion_display, or back in cryoSPARC to avoid wasting time
> by extracting with wrong coordinates. They can also be verified by running
> 2D classification again, but it's less efficient.
> 
> The same issue will also affect the use of an empirical gain reference
> produced by relion_estimate_gain. If your data is from a Gatan camera, you
> will need to use the opposite gain flip (in Y) vs. the gain saved from DM
> and converted by e2proc2d.py (EMAN2) or dm2mrc (IMOD).
> 
> More details, discussion, examples, etc. can be found on the pyem issue
> tracker and wiki on github.
> https://urldefense.com/v3/__https://github.com/asarnow/pyem__;!!Mih3wA!EYimMhBqGpR-E8kdz4pCHVhY8OP3Wtu9MEGXvKoqvtg0EkWO-hj_3sjrEvrsXcSDRyJeEfdF_W7XlDbyP5k$
> 
> Best,
> -da
> 
>> On Thu, Oct 16, 2025 at 10:55?AM Lauren Pellows via 3dem <
>> 3dem at ncmir.ucsd.edu> wrote:
>> 
>> Hi all,
>> 
>> I am new to cryoEM field and have been working in Cryosparc for all my
>> processing. I am now wanting to use Relion and have been trying to figure
>> out how to import the particles I extracted in cryosparc into relion. I
>> wanted to reprocess my raw micrographs in relion so I imported those ran
>> motion correction and CTF estimation on those. After that I ran csparc2spar
>> on my cryosparc data and now have my particles in a .star file. I also have
>> gone into the particle.star file made sure the _rlnMicrographName in the
>> star file to match the relion processes images. I have now imported the
>> particles.star file into relion but when I run the extraction job I don't
>> get any extracted particles.
>> 
>> I have been reading online and can't find anything conclusive on if I need
>> to run the extraction job. I have read that I dont need run the extraction
>> job since the particles.star file should have all the metadata on the
>> particles, and I can just use the particles.star to run my jobs. I also
>> read that I can rerun the extraction job using the particle coordinates
>> from cryosparc. Since these feel counter intuitive and I keep getting
>> errors I am not sure what to do next. I know that this is a very typically
>> workflow that people do so im hoping this is a pretty straightforward
>> question. Any help or advice anyone has would be a great help!!
>> 
>> Thank you so much,
>> 
>> Lauren Pellows, PhD
>> 
>> Postdoctoral Fellow
>> Dukovic Lab
>> University of Colorado, Boulder
>> 
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>> 
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> End of 3dem Digest, Vol 218, Issue 24
> *************************************