LST file to TIFF

[S. Saif Hasan]

Hello,

I have generated an EMAN2 LST file with negatively stained virus particles. Is there a way to export the particles as individual TIFF files? This is for a teaching assignment in image processing. Thank you.

Saif

[Steve Ludtke]

Sure:

- Extract the particles in the usual way as a per-micrograph .hdf stack (standard tutorial process)

- Run CTF autoprocessing on the particles (note that amplitude contrast should probably be set to 40-60% for neg stain). Do this even if you don't want to use phase-flipped images.

- you should now see a set of .lst files (similar to .star files, but more flexible) in the sets/ folder

- e2proc2d.py sets/<appropriate .lst file>  ptcls.tif  --unstacking

this will produce a numbered stack of individual particle images in tiff format.

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[S. Saif Hasan]

Hello Steve,

I followed the instructions but the TIFF files that are generated do not show any particles. Onee of the images so generated is attached as an example. Any advice would be greatly appreciated. Thanks.

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Saif

S. Saif Hasan

Urbana, Maryland, USA

[Steve Ludtke]

How did you display the TIFF?  Try opening the TIFF with e2display and see if it looks ok there. Some TIFF readers don't support all of the features/modes TIFF files can have. The default mode for TIFF files in EMAN2 is floating point greyscale, which preserves the original values. You can force the output mode to 8 or 16 bit integer instead, which will improve compatibility, but potentially have some data loss depending on the source.

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<WTptcls-413.tif>

[S. Saif Hasan]

Hello Steve,

Thanks for the suggestion. e2display.py works quite well. Other software seem to be a problem. I will check with students to see if they are OK using e2display.py 

To view this discussion visit https://groups.google.com/d/msgid/eman2/202E9349-C16A-4919-829C-869A339B81A3%40gmail.com.

[Steve Ludtke]

Hi, 

you can generate more compatible tiffs by specifying

--outmode uint8

or 

--outmode uint16

as part of the e2proc2d.py command line

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[S. Saif Hasan]

Hello Steve,

Thank you. This is extremely helpful. 

Does the coordinate system in eman2 start at 0,0 or 1,1, and where is this reference point located in the micrograph? The students would like to extract the particles on their own. Thank you. 

To view this discussion visit https://groups.google.com/d/msgid/eman2/161CA54B-EAED-4823-B793-371843183FB7%40gmail.com.

[Steve Ludtke]

All indices follow python conventions (zero is the first index)

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