And actually, I just realized the authors have another article which might be more relevant than the one I just linked:<br><br><a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-4NS2GHH-B&_user=1010281&_coverDate=05%2F18%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050264&_version=1&_urlVersion=0&_userid=1010281&md5=7ee12fd37f3f16b1609426fd70b456d4">
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-4NS2GHH-B&_user=1010281&_coverDate=05%2F18%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050264&_version=1&_urlVersion=0&_userid=1010281&md5=7ee12fd37f3f16b1609426fd70b456d4
</a><br><br>Title: "<span class="articleTitle">High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology</span>"<br><br>Abstract: The Mouse Biomedical Informatics Research Network (MBIRN) has been
established to integrate imaging studies of the mouse brain ranging
from three-dimensional (3D) studies of the whole brain to focused
regions at a sub-cellular scale. Magnetic resonance (MR) histology
provides the entry point for many morphologic comparisons of the whole
brain. We describe a standardized protocol that allows acquisition of
3D MR histology (43-ìm resolution) images of the fixed, stained mouse
brain with acquisition times < 30 min. A higher resolution protocol
with isotropic spatial resolution of 21.5 ìm can be executed in 2 h. A
third acquisition protocol provides an alternative image contrast (at
43-ìm isotropic resolution), which is exploited in a statistically
driven algorithm that segments 33 of the most critical structures in
the brain. The entire process, from specimen perfusion, fixation and
staining, image acquisition and reconstruction, post-processing,
segmentation, archiving, and analysis, is integrated through a
structured workflow. This yields a searchable database for archive and
query of the very large (1.2 GB) images acquired with this standardized
protocol. These methods have been applied to a collection of both male
and female adult murine brains ranging over 4 strains and 6 neurologic
knockout models. These collection and acquisition methods are now
available to the neuroscience community as a standard web-deliverable
service.<br><br><br><br><div><span class="gmail_quote">On 7/11/07, <b class="gmail_sendername">Neil Halelamien</b> <<a href="mailto:neilh@caltech.edu">neilh@caltech.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Also, some of the things which distinguish this from a typical clinical MRI and various other notes:<br><br>* unlike a lot of other mouse brain MRI research, the brains were left inside the cranium, preventing structural distortion/damage
<br>* the brains were fixed and treated with an MRI contrast agent<br>* they used a 9.4T magnet (in contrast, typical clinical MRI is maybe 1-3T)<br>* if I understand correctly, algorithms were then used to automatically segment the different brain areas (33 total) apart from each other, and the area data from the 6 brains was combined to form the atlas
<br>* in general, the research is kind of neat, combining a number of already-existing techniques to create a useful atlas<div><span class="e" id="q_113b6eaf6f490f20_1"><br><br><div><span class="gmail_quote">On 7/11/07,
<b class="gmail_sendername">Neil Halelamien</b> <
<a href="mailto:neilh@caltech.edu" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">neilh@caltech.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The NeuroImage article is here, although I think it requires an institutional subscription:
<br><br><a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-4NX8MST-7&_user=1010281&_coverDate=06%2F07%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050264&_version=1&_urlVersion=0&_userid=1010281&md5=0d9d038b1101b4c523e05e0c7cdcd4e3" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-4NX8MST-7&_user=1010281&_coverDate=06%2F07%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050264&_version=1&_urlVersion=0&_userid=1010281&md5=0d9d038b1101b4c523e05e0c7cdcd4e3
</a><br><br>Here's the abstract: <br>Magnetic resonance microscopy (MRM), when used in conjunction with active staining, can<br>produce high-resolution, high-contrast images of the mouse brain. Using MRM, we imaged in
<br>situ the fixed, actively stained brains of C57BL/6J mice in order to characterize the<br>neuroanatomical phenotype and produce a digital atlas. The brains were scanned within the<br>cranium vault to preserve the brain morphology, avoid shape distortions, and to allow an
<br>unbiased shape analysis. The high-resolution imaging used a T1-weighted scan at 21.5 mm<br>isotropic resolution, and an eight-echo multiecho scan, post-processed to obtain an enhanced T2<br>image at 43 mm resolution. The two image sets were used to segment the brain into 33
<br>anatomical structures. Volume, area, and shape characteristics were extracted for all segmented<br>brain structures. We also analyzed the variability of volumes, areas and shape characteristics.<br>The coefficient of variation of volume had an average value of
7.0. Average anatomical images<br>of the brain for both the T1 weighted and T2 images were generated, together with an average<br>shape atlas, and a probabilistic atlas for 33 major structures. These atlases, with their associated
<br>metadata, will serve as baseline for identifying neuroanatomical phenotypes of additional strains,<br>and mouse models now under study. Our efforts were directed toward creating a baseline for<br>comparison with other mouse strains and models of neurodegenerative diseases.
<div><span><br><br><div><span class="gmail_quote">On 7/10/07, <b class="gmail_sendername">John K Clark</b> <<a href="mailto:jonkc@att.net" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
jonkc@att.net</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Some scientists at Duke University have made a MRI image of a mouse<br>brain with "100,000 times higher resolution than a clinical MRI scan".<br>100,000!<br><br><a href="http://www.sciencedaily.com/releases/2007/07/070709145329.htm" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://www.sciencedaily.com/releases/2007/07/070709145329.htm</a><br><br> John K Clark<br><br><br><br><br>_______________________________________________<br>extropy-chat mailing list<br><a href="mailto:extropy-chat@lists.extropy.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
extropy-chat@lists.extropy.org</a><br><a href="http://lists.extropy.org/mailman/listinfo.cgi/extropy-chat" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://lists.extropy.org/mailman/listinfo.cgi/extropy-chat
</a><br></blockquote></div><br>
</span></div></blockquote></div><br>
</span></div></blockquote></div><br>