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

Shi PhD, Dan shid at janelia.hhmi.org
Wed Jan 30 08:17:12 PST 2013

Hi Bob,
Thanks for your message and information,
To now, we know there are several packages can convert emi or ser format
to popular Cryoem formats with or without specific instruction. But I
don't know if Tia save one image to two files is normal.
If FEI is willing to improve Tia, the issue would be solved at the root
for all of Tia users. If modifying Tia is a major upgrade or too difficult
to its software develop team, we have to do whatever to process the data
with extra steps.
We all appreciate the groups who have devoted their time and effort to
develop the converting software,
Kind regards,


On 1/30/13 10:09 AM, "Bob Grassucci" <rg2502 at columbia.edu> wrote:

>Hi Dan,
>While working on AutoEmation in our lab which runs in the TIA
>environment  Jianlin Lei asked how we could output mrc files and the
>answer was that we needed the file tecnaitomo.dll which is a com
>component that needs to be registered.  From there AutoEMation output
>was mrc files.  I have copied Jianlin on this message. Perhaps he can
>comment.  I believe there is also a cp from emi command in spider
>assuming the file format has not changed since 2002.
>On 1/29/2013 3:54 PM, Shi PhD, Dan wrote:
>> Dear colleagues,
>> This message is to whom may concern FEI Falcon/Eagle cameras (made by
>> which use Tia to control, if you're not interested in using Tia
>> 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
>> 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
>> 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
>> 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.
>> 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
>>> If you are processing in EMAN2 you can just start with the .ser files
>>> 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
>>> format.
>>> Sincerely,
>>> Jason Kaelber_______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
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