Converting TIF files for processing in cisTEM

3 posts / 0 new

Wed, 07/11/2018 - 13:55

erikklontz

Hi All,

I'm new to EM and getting started by doing some negative stain. The problem I'm running into is our microscope (Tecnai T12 TEM) outputs images as TIF files. I'd like to create 2D class averages, and potentially some low resolution 3D models of the negative stain images using cisTEM, but my understanding is cisTEM only reads in MRC files. I can convert my TIF files to MRC using the program em2em, but it seems that the conversion introduces some major artifacts that make CTF correction and particle picking impossible. Has anyone encountered this or know of a solution?

For reference, I've attached images of the original TIF file, how cisTEM views the file once I've converted it to an MRC and attempted a CTF correction, and how the file looks after I've converted the MRC back to a TIF.

I appreciate any advice!

Thanks,
Erik

File:

Original_tif.tif

cisTEM_mrc_view.png

Converted_back_to_tiff.tif

Wed, 07/11/2018 - 14:59

alexis

Hi Erik,

Thanks for trying cisTEM!

Looks like the conversion from TIF to MRC may have failed because of endianess or bit depth issues. Perhaps you should try IMOD's tif2mrc program instead?

Cheers,

Alexis

Wed, 07/11/2018 - 15:43

erikklontz

Thanks Alexis, this did the

Thanks Alexis, this did the trick! On a related note, does cisTEM recognize MRC image stacks? This seems to be the default output of IMOD's tif2mrc, but when I load it into cisTEM, I can only view the first image in the stack. I got around this by converting the images one at a time and loading them into cisTEM individually.

Thanks,

Erik