[3dem] [TEM] amplitude contrast

Tue Aug 15 06:09:56 PDT 2017

Funny coincidence (I was unaware) but then... I better go back to something
more useful :)

On Tue, Aug 15, 2017 at 2:44 PM, Dominika Elmlund <
dominika.elmlund at monash.edu> wrote:

> Hi Sacha,
> Philip did his PhD with R Schroeder.
> Cheers,
> Dominika
>
> --
> *DOMINIKA ELMLUND PhD *
> Associate Professor
> ARC DECRA Fellow
>
> *ARC Centre of Excellence for Advanced Molecular Imaging*
> *Dept. of Biochemistry and Molecular Biology*
> Monash University
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> simplecryoem.com
>
> On 15 August 2017 at 22:29, Sacha De Carlo <sacha.decarlo at dectris.com>
> wrote:
>
>> ...thus my statement with a "may provide" instead of "will" (provide
>> answers to...).
>>
>> Alright, let's try this again, forward 8 years (2000), Angert et al,
>> zero-loss (no inelastic scattering) and of course in a practical sense the
>> ice thickness and size of the aperture DO influence the contrast (for the
>> same defocus or in-focus image), but I do not recall other papers where it
>> was quantified methodically (thoroughly)...
>>
>> Cheers,
>> Sacha
>>
>>
>>
>> On Tue, Aug 15, 2017 at 2:22 PM, Philip Koeck <Philip.Koeck at ki.se> wrote:
>>
>>> Hi Sacha.
>>>
>>>
>>>
>>> Thanks for the paper.
>>>
>>>
>>>
>>> I don’t think Wade says very much about the source of amplitude contrast.
>>> He lists some possible explanations from other publications in section 2
>>> of the paper,
>>>
>>> but to me it sounds a bit like nobody is really sure.
>>> Therefore Wade and many others just continue with a phenomenological
>>> description.
>>>
>>> I see many open questions:
>>> If it’s due to scattering outside the aperture, shouldn’t it depend
>>> strongly on the aperture size?
>>> If it’s due to multiple scattering, it must depend strongly on specimen
>>> thickness.
>>>
>>> If it’s due to inelastic scattering, why is it so weak (about 10%)?
>>> Inelastic scattering has a larger cross section than elastic, I believe.
>>>
>>>
>>>
>>> All the best,
>>>
>>>
>>>
>>> Philip
>>>
>>>
>>>
>>>
>>>
>>> *Från:* Sacha De Carlo [mailto:sacha.decarlo at dectris.com]
>>> *Skickat:* den 15 augusti 2017 13:11
>>> *Till:* Philip Koeck
>>> *Kopia:* 3dem at ncmir.ucsd.edu
>>> *Ämne:* Re: [3dem] [TEM] amplitude contrast
>>>
>>>
>>>
>>> A good reference which may provide you with an answer... I am sure many
>>> other people will provide more recent studies...
>>>
>>>
>>>
>>> Enjoy !
>>>
>>>
>>>
>>> Best,
>>>
>>> Sacha
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Tue, Aug 15, 2017 at 12:55 PM, Philip Koeck <Philip.Koeck at ki.se>
>>> wrote:
>>>
>>> Dear all.
>>>
>>>
>>>
>>> Is there any agreement on the cause of amplitude contrast when imaging
>>> proteins in cryo-TEM?
>>>
>>>
>>>
>>> Is it the second order term in the expansion of a weak phase object or
>>> is it due to inelastic scattering or the aperture or something else?
>>>
>>>
>>>
>>> Al the best.
>>>
>>>
>>>
>>> Philip
>>>
>>>
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>>>
>>>
>>>
>>>
>>> --
>>>
>>> Sacha De Carlo, Ph.D.
>>>
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>>
>>
>>
>> --
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Sacha De Carlo, Ph.D.
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