[3dem] Falcon 3 output
Takanori Nakane
tnakane.protein at osaka-u.ac.jp
Fri Jan 6 14:40:07 PST 2023
Hi,
In counting mode images from Falcon3 written in MRC (not EER),
one electron is rendered as a 3x3 pixel blob that sums to 100.
This is why Falcon movies do not compress well.
(I have been asking TFS to add an option to render one electron
as 1 for many years...)
https://urldefense.com/v3/__https://relion.readthedocs.io/en/release-3.1/Reference/MovieCompression.html*falcon3-falcon4__;Iw!!Mih3wA!D3GRVMU_kS7Y6Jdb6GVPj_pB-WRlDwY7YkckrRxtmNYwptzEA4-k9rQx9u6KehIkptjiB2Kqd5_VhsssAAr8SxfermI7QC-5Lr0$
Thus, "mean = 2382" corresponds to 24 e/px, consistent with
your expectation "20 - 25 electrons per pixel".
Best regards,
Takanori Nakane
On 2023/01/07 3:06, Morgan, David Gene 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:
>
> 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!D3GRVMU_kS7Y6Jdb6GVPj_pB-WRlDwY7YkckrRxtmNYwptzEA4-k9rQx9u6KehIkptjiB2Kqd5_VhsssAAr8SxfermI7vOExvxU$
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