Image imports incorrectly from Focus

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#1

Hi our lab has been using Focus to prescreen our data. We’ve noticed that when we import the data sometimes the image isn’t read by cryosparc correctly and puts the left edge of the image somewhere areound the middle. This yields a big black bar down the image were its essentially wrapped the left and right edges of the image to meet. Has anyone else seen this and know how to fix it?


#2

Hi @hansenbry,

Can you check if the output data from Focus is in a non-standard format (MRC mode) or if there is an extended header?

Ali


#3

Hi @apunjani here is the output of the header info:

[hansenbry@D01868462 stackaligned]$ header FoilHole_19850809_Data_19848978_19848979_20190221_0328_Fractions_aligned.mrcs

RO image file on unit 1 : FoilHole_19850809_Data_19848978_19848979_20190221_0328_Fractions_aligned.mrcs Size= 4128776 K

Number of columns, rows, sections … 4096 4096 63
Map mode … 2 (32-bit real)
Start cols, rows, sects, grid x,y,z … 0 0 0 4096 4096 63
Pixel spacing (Angstroms)… 0.8585 0.8585 0.8585
Cell angles … 90.000 90.000 90.000
Fast, medium, slow axes … X Y Z
Origin on x,y,z … -0.000 -0.000 -0.000
Minimum density … 0.0000
Maximum density … 0.0000
Mean density … 0.0000
RMS deviation from mean… 0.0000
tilt angles (original,current) … 0.0 0.0 0.0 90.0 90.0 90.0
Space group,# extra bytes,idtype,lens . 0 8064 5 0

 0 Titles :

      Tilt axis rotation angle =     0.0

#4

It looks like these files do have an extended header of 8064 bytes (http://www.ccpem.ac.uk/mrc_format/mrc2014.php). We will be rolling out the fix for this in the next release!