Hi,
Sorry, I was not clear. Thanks for pointing it out.
I meant the quality of motion correction is the same for the
following two strategies:
(1) saving gain-non-corrected movies and the gain reference
separately and applying the gain correction during
data processing
(2) saving gain corrected movies during data collection
> My recommendation would be keep the uncorrected (compressed if you want)
> images for storage efficiency,
Yes.
> and always correct for the gain before doing any operation with those
movies
> movies (the corrected version can be
> deleted after finishing the operation so that it does not take space).
In most programs, this is done in memory, so users don't have to
write (huge) gain-corrected movies during data processing.
Of course, they must specify the gain reference and geometry
transformations (rotations and flipping) if applicable.
Best regards,
Takanori Nakane
On 2018/12/16 3:21, Carlos Oscar S. Sorzano wrote:
> Dear Bum and Takanori,
>
> El 12/12/2018 a las 9:02, Takanori Nakane escribió:
>> Hi,
>>
>> The advantage of non-gain-corrected data is that it is easier to
>> compress.
> I totally agree with this.
>> The quality of motion correction is the same.
>
> I would disagree with this statement. Depending on the range of the gain
> image (case 1: from 0.999 to 1.001; or case 2: from 0.5 to 2), the movie
> alignment may be driven by the particles in the image (case 1) or by the
> gain image (case 2, in this case I would expect that the alignment
> algorithm does not want to move the images at all because it would mean
> disaligning the gain images which have a lot of energy).
>
> My recommendation would be keep the uncorrected (compressed if you want)
> images for storage efficiency, and always correct for the gain before
> doing any operation with those movies (the corrected version can be
> deleted after finishing the operation so that it does not take space).
>
> Kind regards, Carlos Oscar
>
>>
>> Unfortunately, you cannot save non-gain corrected data from Falcon.
>> It is available only for K2/K3.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2018/12/12 2:58, 류범한 wrote:
>>> Hello, CCPEM.
>>>
>>> So far I have always collected gain-corrected data with EPU (& Titan
>>> Krios+Falcon3 / FEI).
>>>
>>> But in somewhere I read that ‘non-gain-corrected data' would be
>>> better in motion tracking with separately prepared gain reference
>>> image. So I am about to check how much it would be helpful, but I
>>> never tried this before.
>>>
>>> Regarding this, I have several questions.
>>>
>>>
>>> 1. What is the actual advantage of ’non-gain-corrected data’? in what
>>> terms exactly?
>>> (Simply tracking algorithms of motion correction softwares are
>>> slightly better than EPU?)
>>>
>>> 2. In practice, how much is it advantageous? in what terms?
>>> (Especially in the aspect of final resolution of refined 3D map)
>>>
>>> 3. How can I collect non-gain-corrected data ?
>>> By selecting ‘Bias’ option of Bias/Gain correction setting in CCD/TV
>>> camera TAB on TEM user interface?
>>>
>>> 4. How can I prepare gain reference separately and correctly?
>>> - Simply take from Falcon Reference manager? But file extension is
>>> .RAW other than .mrc. :(
>>> - Set the imaging condition exactly same with that of data
>>> collection, and just take gain reference image w/o sample or in empty
>>> hole area? (then check it via TIA?)
>>>
>>>
>>> Thanks in advance.
>>>
>>>
>>>
>>> Bum Han Ryu
>>>
>>> Postdoctoral Researcher
>>> Korea Basic Science Institute (KBSI)
>>> 161 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si
>>> Chungcheongbuk-do, Republic of Korea
>>>
>>> Office) +82-43-240-5329
>>> Mobile) +82-10-7119-0505
>>>
>>>
>>>
>>>
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