[3dem] Falcon 3 output

[Takanori Nakane]

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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