Dear Joshua,

A little bit more detail: for the K2, the gain normalization image tells you which pixels tend to count too many electrons and which pixels tend to count too few electrons. After applying the gain normalization, a pixel that was found to count more than the true number of electrons (e.g. by 3%), which registered a total of  5 electrons during the exposure, will have the 5 replaced by 4.85 (0.97 x 5). As 4.85 is no longer a natural number, it cannot easily be stored as an 8 bit integer. As strange as this sounds, it is the correct thing for the Gatan camera to do. Therefore, only the non-gain corrected movie can be stored as 8 bit without loss of information.

I’m not exactly sure what the Falcon 3 in counting mode is storing - the gain normalized images are 16 bit integers but the numbers are too large to be counts. I think it is (1) doing something to avoid aliasing without requiring the user to Fourier crop images (a good thing) and (2) scaling the counts by some amount in order to store non-integers after gain correction as large integers (see above, for example representing 4.85 as 485). I don’t think movies these can be converted to 8 bit integers without loss of information.

Best,
John

-- 
John Rubinstein
Molecular Medicine Program
The Hospital for Sick Children Research Institute
686 Bay Street, Rm. 20-9705
Toronto, ON
Canada
M5G 0A4
Tel: (+001) 416-813-7255
Fax: (+001) 416-813-5022
www.sickkids.ca/research/rubinstein

On Sep 11, 2017, at 1:29 PM, Joshua Lobo <[log in to unmask]> wrote:

Hi Dr Rubinstein and  CCPEM

I have a question  regarding an old thread (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCPEM;9cb5696c.1506). I haven't been able to find a good explanation regarding this in the context of the Falcon-3 . Is the "natural counting " that you described  only pertaining the K2 or is this also true for the Falcon-3 in Electron Counting mode?

As Far as I am aware EPU that comes with the Falcon-3  cannot record an 8 bit movie . Compression of the movie is always possible but if there is a better way I would like to understand it .

Sincerely
Joshua Lobo