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<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Benjamin,<o:p></o:p></span></a></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">We recently published a paper on how to measure the anisotropy in electron tomograms (</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/25843950"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">http://www.ncbi.nlm.nih.gov/pubmed/25843950</span></a><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">).
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).
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Roman<o:p></o:p></span></p>
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<p class="MsoNormal" align="center" style="text-align:center"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:gray">Dr. R.I.Koning (Roman)<o:p></o:p></span></b></p>
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<p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray">Department of Cell Biology, Leiden University Medical Center
</span><span lang="EN-US" style="font-size:8.0pt;font-family:"Calibri","sans-serif";color:gray"><o:p></o:p></span></p>
<p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray">Postal Zone S1-P, P.O.Box 9600, 2300 RC Leiden, The Netherlands<o:p></o:p></span></p>
<p class="MsoNormal" align="center" style="text-align:center"><b><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray">visiting address</span></b><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray">:</span><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray">
Einthovenweg 20, Building 2, zone S1-P, room R-90-20<o:p></o:p></span></p>
<p class="MsoNormal" align="center" style="text-align:center"><b><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray">tel.</span></b><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray"> (31)
71 526 9296 <b>fax.</b> (+31) 71 526 8270 <b>mail.</b> r.i.koning@lumc.nl <b>web.</b> electronmicroscopy.lumc.nl</span><span lang="EN-US" style="font-size:8.0pt;color:gray"><o:p></o:p></span></p>
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<p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray">Netherlands Centre for Electron Nanoscopy, Institute Biology Leiden, Leiden University<o:p></o:p></span></p>
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Einsteinweg 55, 2333 RC Leiden, The Netherlands, room 05.11<o:p></o:p></span></p>
<p class="MsoNormal" align="center" style="text-align:center"><b><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray">tel.</span></b><span lang="EN-US" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray"> (31)
71 527 1423 <b>mail.</b> r.i.koning@biology.leidenuniv.nl <b>web.</b> www.necen.nl<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> 3dem [mailto:3dem-bounces@ncmir.ucsd.edu]
<b>On Behalf Of </b>Benjamin Himes<br>
<b>Sent:</b> maandag 24 augustus 2015 15:44<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> [3dem] Anisotropic resolution<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p>Dear colleagues,<o:p></o:p></p>
<p>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.<o:p></o:p></p>
<p>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?
<o:p></o:p></p>
<p>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.<o:p></o:p></p>
<p>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.<o:p></o:p></p>
<p>Many thanks,<o:p></o:p></p>
<p>Benjamin Himes<o:p></o:p></p>
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