[3dem] Exporting Selected Motion-Corrected Micrographs from RELION to CryoSPARC

[Daniel Asarnow]

Hi Scott,
You can use the "import micrographs" job to import micrographs into
cryoSPARC using an appropriate wildcard or by creating symbolic links in a
new directory. For example, in the relion project directory:
mkdir csimport; cd csimport
for i in $(relion_star_printtable ../selected_micrographs.star
data_micrographs rlnMicrographName); do ln -s ../$i -t .; done
You will have to run CTF estimation again in cryoSPARC, however fortunately
1) it is cheap and 2) Patch CTF is in my experience superior even to
per-particle estimates unless the particles are quite large or there is
significant residual beam tilt.

Best,
-da

On Thu, Jun 26, 2025 at 10:08 AM justacuriousone01--- via 3dem <
3dem at ncmir.ucsd.edu> wrote:

> Dear 3DEM community,
>
> I’m looking for a way to export a subset of micrographs—already
> motion-corrected and CTF-estimated in RELION—for further processing in
> CryoSPARC, starting from Patch Motion Correction.
>
> Is there an easy or recommended method to transfer selected micrographs
> between the two softwares? If anyone knows of a script or best practice for
> this workflow, I’d really appreciate your help.
>
> Kind regards,
> Scott
>
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