[3dem] Re: file conversion (aaron smith)

Mike Strauss mikestrauss13 at crystal.harvard.edu
Wed Jan 30 08:48:53 PST 2013


Hi Dan,

thanks for bringing up this point.  It seems the FEI does have the software to output something akin to mrc files.  The EPU package outputs 3 files per image: a small version of the image in jpeg format, an xml file containing parameters of the data acquisition, and the data image as an mrc file, though it does not adhere to the mrc or ccp4 standard.  The mrc files that are produced can be displayed with a number of software packages (bsoft, EMAN2, IMOD are the ones that I tried), but cannot be read, and throw an error by the mrc programs of image2010.  The header is not correctly populated (you can find the output of the IMOD header command below (the mrc header command fails).

Given that FEI has, in some sense, heard the call to at least give the option of using a standard file format, such as mrc, for ease of use in processing, it would be nice if this feature were available across the board, both in TIA and in other places.  I would also prevail upon the good folk of FEI monitoring this thread to implement the existent mrc support fully according to the mrc/ccp4 standard (which includes pixel size, axis indices, origin position and density values).  While I commend them for the excellent ideas they have brought forth with the additional jpg and xml files, it would be very helpful to see the implementation carried through to completion.

Regards,

mike


RO image file on unit   1 : moo.mrc     Size=      32897 K

                    This file has an old-style MRC header.

         This file has invalid axis indices, adjusting them to 1,2,3

 Number of columns, rows, sections .....    4096    4096       1
 Map mode ..............................    6   (unsigned 16-bit integer)  
 Start cols, rows, sects, grid x,y,z ...    0     0     0       1      1      1
 Pixel spacing (Angstroms)..............   1.000      1.000      1.000    
 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                               
 tilt angles (original,current) ........   0.0   0.0   0.0   0.0   0.0   0.0
 Space group,# extra bytes,idtype,lens .        0   131072        0        0

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Extended header from SerialEM contains:




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