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

Joaquin Oton joton at cnb.csic.es
Wed Jan 30 00:11:28 PST 2013

Dear colleagues,

Xmipp3.0 also supports .ser files as input for any of its programs and 
protocols. Anyway, these files can also be converted to standard .tiff 
or .mrc using  the xmipp_image_convert command.

kind regards,

On 01/29/2013 09:54 PM, Shi PhD, Dan wrote:
> 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
>> format.
>> Sincerely,
>> Jason Kaelber_______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
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Joaquín Otón Pérez

Biocomputing Unit
National Center of Biotechnology (CSIC)
Campus Universidad Autónoma de Madrid (Cantoblanco)
28049 Madrid (Spain)

Tlf: (34) 91 585 45 10
Fax: (34) 91 585 45 06

email: joton at cnb.csic.es
web: http://biocomp.cnb.csic.es

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