[3dem] Anisotropic resolution

R.I.Koning at lumc.nl R.I.Koning at lumc.nl
Fri Sep 4 07:50:52 PDT 2015


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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