[3dem] 3dem Digest, Vol 185, Issue 9
Anchi Cheng
acheng at nysbc.org
Fri Jan 6 12:22:30 PST 2023
Hi, Gene,
The Falcon mrc frames as well as the sum are gain-corrected, expressed as you see
as integer. Gain correction of anything from 0.50000001-1.4999999 would have made a count of 1 comes back still as 1
when expressed as integer, so that is not desirable.
Therefore, the data are scaled so that it can give you a better representative of the corrected
effect.
The scaling is determined by the camera software in the file Wim indicated.
Anchi
> On Jan 6, 2023, at 12:00 PM, 3dem-request at ncmir.ucsd.edu wrote:
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> Today's Topics:
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> 1. Falcon 3 output (Morgan, David Gene)
> 2. Re: Falcon 3 output (Wim Hagen)
>
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 6 Jan 2023 18:06:39 +0000
> From: "Morgan, David Gene" <dagmorga at indiana.edu>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: [3dem] Falcon 3 output
> Message-ID:
> <BN8PR08MB64045DDE76E140C589B3A140D0FB9 at BN8PR08MB6404.namprd08.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I have a stupid question about the MRC files output by our Falcon 3 camera. I just acquired a set of movies in counting mode where the total dose should be on the order of 25 electrons/ A^2, spread over 22 frames. My pixel size is just under 1 A, so my images should have on the order of 20 - 25 electrons per pixel. At least the average over all the pixels after summing or motion correction should be close to that...
>
> When I examine the MRC files output by EPU, I find the following min/max/mean for an example acquisition:
>
> 1. file with fractions (22 frames): min = 0, max = -1, mean = -2 (obviously bogus values)
> 2. fractions after recalculating min/mix/mean: min = -23, max = 549, mean = 108.27
> 3. summed image (non-motion corrected single frame output by EPU): min = 1239, max = 3809, mean = 2382
>
> My stupid question: How do these numbers relate to what should be the counted number of electrons that hit the specimen?
>
> I suspect that I am seeing some stupid effect of an "average counts per electron" in these images, but I had previously (and I suppose foolishly) assumed that in counted mode images, one count would mean one electron...
>
> Thanks for any input you can offer, and Happy New Year.
>
> --
> politics is more difficult than physics.
> A. Einstein
>
> David Gene Morgan
> Electron Microscopy Center
> 047E Simon Hall
> IU Bloomington
> 812 856 1457 (office)
> 812 856 3221 (3200)
> https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!E-FcoZUZdcr3llQ_tQ7nra_aC45SHHOofl5vsdk4RilKOYWBacUzdW1K8BzGLp3U7LbXIfTjwt3E1eA8hKRTl-Y$
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> Message: 2
> Date: Fri, 6 Jan 2023 19:23:32 +0100
> From: Wim Hagen <hagen at embl.de>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Falcon 3 output
> Message-ID: <33C1C3E5-665F-4144-933B-6F04BAB14758 at embl.de>
> Content-Type: text/plain; charset="us-ascii"
>
> David,
>
> The conversion rate for counting mode is mentioned in a datasheet of the camera, as a PDF file on some DVD that came with the camera/system.
>
> Best,
>
> Wim
>
>> On 6. Jan 2023, at 19:06, Morgan, David Gene <dagmorga at indiana.edu> wrote:
>>
>> Hi,
>>
>> I have a stupid question about the MRC files output by our Falcon 3 camera. I just acquired a set of movies in counting mode where the total dose should be on the order of 25 electrons/ A^2, spread over 22 frames. My pixel size is just under 1 A, so my images should have on the order of 20 - 25 electrons per pixel. At least the average over all the pixels after summing or motion correction should be close to that...
>>
>> When I examine the MRC files output by EPU, I find the following min/max/mean for an example acquisition:
>> file with fractions (22 frames): min = 0, max = -1, mean = -2 (obviously bogus values)
>> fractions after recalculating min/mix/mean: min = -23, max = 549, mean = 108.27
>> summed image (non-motion corrected single frame output by EPU): min = 1239, max = 3809, mean = 2382
>> My stupid question: How do these numbers relate to what should be the counted number of electrons that hit the specimen?
>>
>> I suspect that I am seeing some stupid effect of an "average counts per electron" in these images, but I had previously (and I suppose foolishly) assumed that in counted mode images, one count would mean one electron...
>>
>> Thanks for any input you can offer, and Happy New Year.
>>
>> --
>> politics is more difficult than physics.
>> A. Einstein
>>
>> David Gene Morgan
>> Electron Microscopy Center
>> 047E Simon Hall
>> IU Bloomington
>> 812 856 1457 (office)
>> 812 856 3221 (3200)
>> https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!D4cKB9uZ513EDXnm2rjYWvHx5q6e6ni85ZacwMWTi26UpzBc3Vgeg5GucEfqEvznRT5vXqju15wnc09p$ <https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!E-FcoZUZdcr3llQ_tQ7nra_aC45SHHOofl5vsdk4RilKOYWBacUzdW1K8BzGLp3U7LbXIfTjwt3E1eA8hKRTl-Y$>_______________________________________________
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