[3dem] Exporting a montage map from SerialEM to a single MRC File

[Huy Bui]

Hi Shujun,

You can stitch the images using imod programs.

Extract coordinate:

extractpieces -mdoc MMM.mrc -output MMM.pl <https://urldefense.com/v3/__http://mmm.pl__;!!Mih3wA!CgW418Ed3sUQKk-APLyCQK26Ph1GivpqPFZfeY9WidVFLs2RVBDfcUxkUXEiRWmHjUbTzCIOeElrIPjsVQ$ >

Generate the blended stack (change to bin 1 if you don't want to bin it)

blendmont -imin MMM.mrc -plin MMM.pl -imout MMM_bin4_montage.mrc -rootname
MMM_bin4 -sloppy -shift -bin 4


Best,
H




On Fri, Feb 6, 2026 at 11:05 AM Garry P Morgan via 3dem <3dem at ncmir.ucsd.edu>
wrote:

> Shujun,
> One way to do this is in SerialEM:  while the map file is loaded on your
> monitor in SerialEM, you can “save to other” under the file drop down menu,
> and select mrc as the format you want. This should work for you, just make
> sure that the map is loaded at full resolution in SerialEM, and not binned.
> cheers
> Garry
>
>
> On Feb 6, 2026, at 5:35 AM, 蔡舒君 via 3dem <3dem at ncmir.ucsd.edu> wrote:
>
> [External email - use caution]
>
> Dear Colleagues,
>
> After collecting a map using SerialEM, the output file (map.mrc) contains
> multiple 2D images (e.g., 169 images with dimensions X × Y × Z = 1024 ×
> 1024 × 1), along with the coordinate information for each image. When I
> open map.mrc in 3dmod, it appears as a single montage map (e.g., X × Y × Z
> = 12088 × 12088 × 1).
>
> Could you please advise on how to save this single montage map as a single
> MRC file (e.g., 12088 × 12088 × 1)?
>
> Best regards,
> Shujun
>
>
>
>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem 
>
>
> _______________________________________________
> 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/20260206/db9d19c1/attachment.html>