[3dem] .raw file format conversion

[Wim Hagen]

Dear Tofayel,

ImageJ:
- 32 bit signed
- Offset 49 bytes
- Little-endian byte order

IMOD, for a 4K image,
"raw2mrc -o 49 -x 4096 -y 4096 -t long -c IntermediateImage_yyyymmdd_xxxxxx_n*.raw"
and then your choice of -u for unsigned integer output or -d to divide by 2, otherwise it will divide by 2.

If you have an IMOD installation somewhere and copy the files listed below to some dedicated folder on the microscope pc, you can convert the raw images to MRC stack on the microscope PC (no cygwin needed):
imodzlib1.dll
libcfshr.dll
libguide40.dll
libhvem.dll
libifcoremd.dll
libifft.dll
libifportmd.dll
libiimod.dll
libiwarp.dll
libjpeg.dll
libmmd.dll
libmrcim.dll
libtiff5.dll
newstack.exe
raw2mrc.exe

These are the two options that worked for me but there are more programs that deal with this raw format.

For future acquisition, the latest FEI EPU version writes the frames in a 16 bit MRC stack and SerialEM also handles Falcon frames conveniently and will write a 16 bit MRC stack, we use both at EMBL on our Krios/Falcon2.

Best,

Wim Hagen
EMBL Heidelberg

On Jun 29, 2014, at 3:51 PM, #AHMED TOFAYEL# <TOFAYEL001 at e.ntu.edu.sg> wrote:

> Dear all,
> 
> I am new to the 3DEM mailing and this is my first mail to the EM community. I will be grateful if some of you could help me. I have a basic question about raw file formats. I have my data in raw format from Falcon2 detector in movie frames but I am unable to convert it to other formats. I tried XMIPP but it says that files are corrupted. I have also tried imageJ and em2em but still unable to convert it. I also tried spider but the converted files look different.
> 
> I hope that some of you also might have encountered the same problem and would have found the ways to deal with it.
> 
> 
> Thanks and hoping to get some help.
> 
> Best regards,
> Tofayel Ahmed
> Graduate Student
> NTU Singapore
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem

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