Importing micrographs: Stack from Serial EM

[Gökhan]

Hi,

I have a 2D image-stack file from Serial-EM. I can open it with "Evaluate & Import Micrographs" from the GUI, and also from the browser if I choose "Show 2D" or "Show Stack" buttons.

But then, when I use "Import micrographs", it gives the following error and fails:

1 images, processing 0-85 stepping by 1
Traceback (most recent call last):
  File "/home/tolung/EMAN2/bin/e2proc2d.py", line 685, in <module>
    main()
  File "/home/tolung/EMAN2/bin/e2proc2d.py", line 272, in main
    if imagelist and (not imagelist[i]):
IndexError: list index out of range

Any suggestions?

Thanks.

[Steven Ludtke]

Does the stack contain multiple micrographs, which you are trying to extract and process independently, or is it something like a DDD movie where you are going to combine the data in some fashion ?

EMAN2 doesn't stack CCD frames normally, since each needs to have a unique identity/name during processing. In addition, the MRC format has a few problems in discriminating between 2-D stacks and 3-D volumes. Some people set a particular flag in the header, other people set a different flag. Still others don't discriminate at all.

e2proc2d.py stack.mrc frames.hdf --unstacking

You might also need   --threed2twod, not sure...

----------------------------------------------------------------------------

Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

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[Gökhan]

Does the stack contain multiple micrographs, which you are trying to extract and process independently, or is it something like a DDD movie where you are going to combine the data in some fashion ?

It is the former. Serial-EM saves each micrograph as a slice.
 

e2proc2d.py stack.mrc frames.hdf --unstacking

This is what I used already, which generated the error I posted.
 

You might also need   --threed2twod, not sure...

This did the trick! I had not tried it since the input was not a 3D volume. I guess Serial-EM generates a header as a 3D volume?

Thanks again and happy holidays.