[3dem] Anisotropic resolution

[Benjamin Himes]

Dear Roman & Misha,

Thank you both for pointing out your respective papers regarding the
subdivision of Fourier space by shells & cones in order to estimate
resolution anisotropy.

Follow up questions:

1) are you concerned with the effect of undersampling an already sparse
transform (particularly in the case of the tomogram work?)

Roman - you report use of 200 cones. Did you try other numbers, and what
did you observe; I would guess the overall pattern to be very similar with
different "resolution" values?

2) both papers reference resolution comparing in either pixel^-1 or nm^-1.
Depending on your answer to question 1, do you think this is appropriate,
or would a relative measure (scale the highest to 1) perhaps be a better
representation.

3) Neither presentation seemed to reflect friedel symmetry. While your
choice of cone axis could result in asymmetric sampling, I find this
curious. Comments?

Thanks again!

Benjamin Himes

Dear Benjamin,



We recently published a paper on how to measure the anisotropy in electron
tomograms (http://www.ncbi.nlm.nih.gov/pubmed/25843950). Though we did not
test this on subtomogram averages it might be useful to have a look at the
paper (in case you did not do that yet).



Best regards,



Roman



*Dr. R.I.Koning (Roman)*



Department of Cell Biology, Leiden University Medical Center

Postal Zone S1-P, P.O.Box 9600, 2300 RC Leiden, The Netherlands

*visiting address*: Einthovenweg 20, Building 2, zone S1-P, room R-90-20

*tel.* (31) 71 526 9296* fax.* (+31) 71 526 8270* mail.* r.i.koning at lumc.nl*
web.* electronmicroscopy.lumc.nl



Netherlands Centre for Electron Nanoscopy, Institute Biology Leiden, Leiden
University

*visiting address:* Einsteinweg 55, 2333 RC Leiden, The Netherlands, room
05.11

*tel.* (31) 71 527 1423* mail.* r.i.koning at biology.leidenuniv.nl* web.*
www.necen.nl





*From:* 3dem [mailto:3dem-bounces at ncmir.ucsd.edu]* On Behalf Of* Benjamin
Himes
*Sent:* maandag 24 augustus 2015 15:44
*To:* 3dem at ncmir.ucsd.edu
*Subject:* [3dem] Anisotropic resolution



Dear colleagues,

I hate to stir the pot on the resolution discussion, however, I have a
question regarding any progress on analyzing the anisotropy potentially
present in a 3d em map.

Aside from some discussion on 3d ssnr, particularly by P.P. and a recent
paper on 3d covariance estimation from J.F. Has anybody tried to implement
a concrete way of assessing this issue?

I am particularly concerned with maps generated from subTomogram averaging
and classification: even with an angular distribution that is well sampled,
I am concerned about the fact that cumulative dose, and increased sample
thickness on tilting create a situation where the individual projections do
not have equivalent SNR and therefore a simple plot of angular
distributions would not accurately reflect the quality of the sampling in
Fourier space.

It seems a 3d SSNR might work, but the interpretation of such a plot,
beyond its "potato" like quality, even in terms of the eigenvalues of the
principle axes is not immediately clear to me.

Many thanks,

Benjamin Himes
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