[3dem] [ccpem] lost gain reference image

Marin van Heel marin.vanheel at googlemail.com
Tue Oct 2 18:21:36 PDT 2018


Dear Carlos Oscar and Dimitry,

Unfortunately, you seem to have missed the point of our Afanasyev 2015 
paper. Our paper does not try to duplicate the "experimentally 
determined Gain image" but tries to normalize the signal from each pixel 
to the same average and the same standard deviation at the exposure and 
contrast level that the data set was recorded. Our approach typically 
improves significantly on standard "/a priori/" flat field/gain  
corrections.

We are not directly interested in generic "gain images" as such and we 
certainly  do not generate "gain images" that have an inverted contrast 
when compared to the other ones you have in Figure #1 of your paper. 
Your comments on our methods are thus not appropriate:  "/T//o the best 
of our knowledge, the only article that addresses a similar problem is 
that of Afanasyev //et al.//(2015). In their work, they assimilate the 
gain of the camera to the standard deviation of each pixel over a large 
number of movies, and they prove this is a successful way of identifying 
dead pixels. However, our results show that this approach does not 
provide a consistent gain estimation (Fig. 1)/."

What you call our "gain image" is - apart from an erroneous contrast 
reversal - actually more similar to the "official" gain image in your 
Fig 1 than does the one generated with your proposed algorithm.  I would 
be interested in knowing what the R2 turns out to be after you correct 
the contrast reversal since it visually is better than yours. It would 
be nice if you could respond to this mailing including that 
information!? By the way how exactly is this R2 metric defined (I could 
not find it anywhere in the paper)?

I would want to suggest you and your colleagues to use the FRC metric to 
prove that your approach does indeed remove the influence of the various 
patterns of your detectors exhibits.

My two cents

Marin

=====================


On 02/10/2018 15:19, Carlos Oscar Sorzano wrote:
> By the way, in our article we compared both methods (ours and Marin).
>
> Kind regards, Carlos Oscar
>
>
> On 01/10/2018 21:23, Marin van Heel wrote:
>> Dear Da,
>>
>> In IMAGIC-4D  you can perform the necessary camera correction! 
>> (https://www.nature.com/articles/srep10317).  It does it better than 
>> any manufactures correction and improves the data significantly even 
>> when performed after using the standard gain correction.
>>
>> Cheers,
>>
>> Marin
>>
>>
>> =====================================================
>>
>> On 01/10/2018 15:36, Da Cui wrote:
>>> Hi all,
>>>     The gain reference image for one dataset was missing by 
>>> accident. In order to achieve a more accurate motioncor result, does 
>>> anyone have idea about how to generate a gain reference image from 
>>> the dataset (around 3k movies)?
>>>     Thank you so much for your help!!!
>>> ---Da
>>>
>>> ######################################################################## 
>>>
>>>
>>> To unsubscribe from the CCPEM list, click the following link:
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>>
>>
>

-- 
==============================================================

     Prof Dr Ir Marin van Heel

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