[3dem] Wrong image size from SerialEM

Subangstrom info at subangstrom.com
Thu Aug 30 03:41:32 PDT 2018

Dear Zongli,

I hope you are well.

I have also seen this issue when GMS crashes. For some reason after the 
crash, the compression of the TIFF will add some extra pixel rows and 
columns to all the TIFFS. The manner in which they are added are around 
the perimeter of each frame. So if we have a row with 7676, row 0 and 1 
will have the extra pixels and row 7679 and 7680 will also have extra 
pixels. In the other direction for 7420, column 0 and 1 will have the 
extra pixels and column 7423 and 7424 will have the extra pixels. It is 
as if there is a 2pixel wide "picture frame" around the image.

I have found that it would be more labor intensive to clip each TIFF so 
instead I would add pixels to the gain reference in order to make it the 
same dimensions as the "corrupt" movies. Making the gain reference 
7680x7424 will allow it to be compatible with the movies and MotionCorr 
will not complain that the gain reference is a different size.

One last thing is that in order to make this problem go away you must 
close serial EM, DM, and power cycle the K2 camera, digitizer and 
processor. Hope it works.




On 8/29/2018 10:12 PM, Zongli Li wrote:
> Dear lists,
> Due to an error from Gatan GMS, half of my data set have a wrong image 
> size (7680x7424). The correct image size and the gain reference image 
> is 7676x7420.
> The image stack were collected on K2 camera set at super resolution, 
> using SerialEM and set to dark gain subtracted and LZW compression.
> I would like to clip the tif stack to 7676x7420 so it matches the size 
> of the gain reference image. What is the correct way to clip the tif 
> stack? (which pixels should be cut off)
> Thanks in advance,
> Zongli
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem

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