Hi,
Counting gain reference = 1/(bin(1/Superres gain reference))
Best,
Wim
> On 8. Aug 2019, at 14:05, Takanori Nakane <[log in to unmask]> wrote:
>
> Hi,
>
> Thanks for information.
>
> The size indicates that EPU saves the gain reference
> in super-resolution even when you are collecting in the
> non-super resolution mode.
>
> I don't know if this is intended behavior or a bug.
> I also don't know what is the best way to down-size the
> super-resolution gain reference into 5760 x 4092 pixels.
> Fourier cropping? Or just summing 2x2 pixels in the real space?
>
> Can somebody on the list comment? Or can you ask this to
> Gatan and TF engineers?
>
> Best regards,
>
> Takanori Nakane
>
>> Hi,
>>
>>
>> No I don't use super resolution.
>>
>>
>> The header from gain is:
>>
>> RO image file on unit 1 :
>> FoilHole_6873894_Data_6874760_6874762_20190807_1659_gain.tiff Size=
>> 68068 K
>>
>> This is a TIFF file.
>>
>> Number of columns, rows, sections ..... 11520 8184 1
>> Map mode .............................. 0 (byte)
>> Start cols, rows, sects, grid x,y,z ... 0 0 0 11520 8184
>> 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 ....................... 255.00
>> Mean density .......................... 127.50
>> tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0
>> 0.0
>> Space group,# extra bytes,idtype,lens . 0 0 0
>> 0
>>
>> 0 Titles :
>>
>> The header from the movie is:
>>
>>
>> RO image file on unit 1 :
>> FoilHole_6873900_Data_6874760_6874762_20190807_1703_fractions.tiff
>> Size= 158758 K
>>
>> This is a TIFF file.
>>
>> Number of columns, rows, sections ..... 5760 4092 37
>> Map mode .............................. 0 (byte)
>> Start cols, rows, sects, grid x,y,z ... 0 0 0 5760 4092
>> 37
>> 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 ....................... 255.00
>> Mean density .......................... 127.50
>> tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0
>> 0.0
>> Space group,# extra bytes,idtype,lens . 0 0 0
>> 0
>>
>> 0 Titles :
>>
>>
>> ________________________________
>> From: Takanori Nakane <[log in to unmask]>
>> Sent: Thursday, August 8, 2019 2:51:43 PM
>> To: Yehuda Halfon <[log in to unmask]>
>> Cc: [log in to unmask] <[log in to unmask]>
>> Subject: Re: [ccpem] The new embedded K3 in EPU gain reference file
>>
>> Hi,
>>
>> I need sample files to investigate this issue.
>>
>> Are you using super-resolution?
>>
>> Can you run IMOD's "header" command on both the gain reference
>> and the movie from EPU?
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>>> Hi all,
>>>
>>> We just got an update for EPU that let us work with K3.
>>>
>>> In it we can now save files in LZW tif without the gain. However the
>>> gain
>>> file is also in tiff and in its size (in pixels) is bigger but the ratio
>>> is the same. Relion complains about it and won't do mcorr. So I resized
>>> it
>>> to the K3 size, converted it to mrc using tif2mrc, and now everything
>>> works fine.
>>>
>>>
>>> I have 2 questions:
>>>
>>> 1) Is the resizing it will make the mcorr run worst?
>>>
>>> 2) Anyone knows if I can save the gain file in mrc in the correct size?
>>> (like from GMS?)
>>>
>>>
>>> Thanks,
>>>
>>>
>>> Yehuda Halfon
>>>
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>>>
>>
>>
>>
>
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