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

Sat Oct 18 12:20:57 PDT 2025

If you're asking why the different origin conventions were used, the short
answer is that one is common in computer vision/computer science (arrays
indices) and one is common in math and microscopy (typical Cartesian
origin).

If you're asking about flipping movies, it is for historical consistency as
explained here.
https://urldefense.com/v3/__https://github.com/3dem/relion/blob/d476e6f6a4f1f37627c06ace5227fc374c0c2b05/src/rwTIFF.h*L227__;Iw!!Mih3wA!B4PpfA5-olcAdsZ7Txcx2XQIaVjOSk9N986inXVXyq0SQprI6xTwc-9tHDGvGSuw-MkJl4pS4C8Q2MnfgFY$ 

Best,
-da

On Fri, Oct 17, 2025 at 12:24 PM Dewight Williams via 3dem <
3dem at ncmir.ucsd.edu> wrote:

> No clue why?
>
> > On Oct 17, 2025, at 12:00 PM, 3dem-request at ncmir.ucsd.edu wrote:
> >
> > Send 3dem mailing list submissions to
> >    3dem at ncmir.ucsd.edu
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
> https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem__;!!IKRxdwAv5BmarQ!aoCpQ7gq7iIUyDaprIYQP3tEiIL2RQ6RRr2F623uLuDLfADYsYAoZT84XwpOnRhoitEqm4CT78V0ybIBVl25xIh7RCz2wAVSeHM_7A$
> > or, via email, send a message with subject or body 'help' to
> >    3dem-request at ncmir.ucsd.edu
> >
> > You can reach the person managing the list at
> >    3dem-owner at ncmir.ucsd.edu
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of 3dem digest..."
> >
> >
> > Today's Topics:
> >
> >   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
> >>
> >> _______________________________________________
> >> 3dem mailing list
> >> 3dem at ncmir.ucsd.edu
> >>
> https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem__;!!IKRxdwAv5BmarQ!aoCpQ7gq7iIUyDaprIYQP3tEiIL2RQ6RRr2F623uLuDLfADYsYAoZT84XwpOnRhoitEqm4CT78V0ybIBVl25xIh7RCz2wAVSeHM_7A$
>
> >>
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> https://urldefense.com/v3/__http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20251016/edcc60db/attachment-0001.html__;!!IKRxdwAv5BmarQ!aoCpQ7gq7iIUyDaprIYQP3tEiIL2RQ6RRr2F623uLuDLfADYsYAoZT84XwpOnRhoitEqm4CT78V0ybIBVl25xIh7RCz2wAUWoj69UQ$
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > 3dem mailing list
> > 3dem at ncmir.ucsd.edu
> >
> https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem__;!!IKRxdwAv5BmarQ!aoCpQ7gq7iIUyDaprIYQP3tEiIL2RQ6RRr2F623uLuDLfADYsYAoZT84XwpOnRhoitEqm4CT78V0ybIBVl25xIh7RCz2wAVSeHM_7A$
> >
> >
> > ------------------------------
> >
> > End of 3dem Digest, Vol 218, Issue 24
> > *************************************
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem 
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20251018/75461248/attachment.html>