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

Shi PhD, Dan shid at janelia.hhmi.org
Tue Jan 29 12:54:43 PST 2013

Dear colleagues,
This message is to whom may concern FEI Falcon/Eagle cameras (made by FEI)
which use Tia to control, if you're not interested in using Tia software,
please ignore it. 

The Tia saves two proprietary files for each image i.e. image.emi and
image_1.ser, they seems to contain the same data with different format;
the program also can export an image to non-standard tif and bin(raw)
formats without header information. Both ser and emi formats are currently
incompatible with most of Cryo-EM data processing packages.  Only two or
three software packages exist which claim capable to convert one of the
two (not both) files into the .mrc or .tif "standard" format, we've tried
all of them, so far, only EMAN2 seems to work. If FEI could modify Tia's
output of each image to a single file with more popular or open format,
like tiff or mrc, it would make the job much easier and save a lot storage
space and time to all Tia user group especially to newer one.

There have been sort of long email communications initialized by one FEI
engineer with me, at the end, he seems not willing to do anything to
improve TIA which was designed for material science over 20 years ago. As
one Cryo-EM community,  we should all insist that FEI devotes a little
extra effort to  improve or upgrade Tia to make our research more
efficiently, which may also benefit FEI's image detector market share.
Thanks for your time,
Kind regards,

Dan Shi, PhD
Senior Scientist
Dr Gonen lab 
HHMI Janelia Farm Research campus
19700 Helix Dr
Ashburn, VA 20147

On 1/21/13 8:19 PM, "Kaelber, Jason Toye" <kaelber at bcm.edu> wrote:

>EMAN2 supports the .ser files that are written alongside the .emi files.
>If you are processing in EMAN2 you can just start with the .ser files as
>if they were .mrc or some other format without any worries. If you are
>not processing in EMAN2 you can use the e2proc2d.py command to convert
>them to some other format. For instance the command "
>e2proc2d.py micrograph_0000.ser micrograph_0000.mrc
>" reads the FEI-format file micrograph_0000.ser and writes it out in MRC
>Jason Kaelber_______________________________________________
>3dem mailing list
>3dem at ncmir.ucsd.edu

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