Automatic identification of gray and white matter components in polarized light imaging
Polarized light imaging (PLI) enables the visualization of fiber tracts with high spatial resolution in microtome sections of postmortem brains. Vectors of the fiber orientation defined by inclination and direction angles can directly be derived from the optical signals employed by PLI analysis. The...
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creator | Dammers, Jürgen Breuer, Lukas Axer, Markus Kleiner, Melanie Eiben, Björn Gräßel, David Dickscheid, Timo Zilles, Karl Amunts, Katrin Shah, N. Joni Pietrzyk, Uwe |
description | Polarized light imaging (PLI) enables the visualization of fiber tracts with high spatial resolution in microtome sections of postmortem brains. Vectors of the fiber orientation defined by inclination and direction angles can directly be derived from the optical signals employed by PLI analysis. The polarization state of light propagating through a rotating polarimeter is varied in such a way that the detected signal of each spatial unit describes a sinusoidal signal. Noise, light scatter and filter inhomogeneities, however, interfere with the original sinusoidal PLI signals, which in turn have direct impact on the accuracy of subsequent fiber tracking. Recently we showed that the primary sinusoidal signals can effectively be restored after noise and artifact rejection utilizing independent component analysis (ICA). In particular, regions with weak intensities are greatly enhanced after ICA based artifact rejection and signal restoration.
Here, we propose a user independent way of identifying the components of interest after decomposition; i.e., components that are related to gray and white matter. Depending on the size of the postmortem brain and the section thickness, the number of independent component maps can easily be in the range of a few ten thousand components for one brain. Therefore, we developed an automatic and, more importantly, user independent way of extracting the signal of interest. The automatic identification of gray and white matter components is based on the evaluation of the statistical properties of the so-called feature vectors of each individual component map, which, in the ideal case, shows a sinusoidal waveform. Our method enables large-scale analysis (i.e., the analysis of thousands of whole brain sections) of nerve fiber orientations in the human brain using polarized light imaging.
► Novel approach to automatically identify gray and white matter components from PLI. ► User independent way of signal enhancement in a large set of PLI images. ► The method includes artifact and noise rejection utilizing ICA. ► Regions with weak intensities are greatly enhanced after ICA. ► Our test statistic is sensitive to both, missing components and changes in SNR. |
doi_str_mv | 10.1016/j.neuroimage.2011.08.030 |
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Here, we propose a user independent way of identifying the components of interest after decomposition; i.e., components that are related to gray and white matter. Depending on the size of the postmortem brain and the section thickness, the number of independent component maps can easily be in the range of a few ten thousand components for one brain. Therefore, we developed an automatic and, more importantly, user independent way of extracting the signal of interest. The automatic identification of gray and white matter components is based on the evaluation of the statistical properties of the so-called feature vectors of each individual component map, which, in the ideal case, shows a sinusoidal waveform. Our method enables large-scale analysis (i.e., the analysis of thousands of whole brain sections) of nerve fiber orientations in the human brain using polarized light imaging.
► Novel approach to automatically identify gray and white matter components from PLI. ► User independent way of signal enhancement in a large set of PLI images. ► The method includes artifact and noise rejection utilizing ICA. ► Regions with weak intensities are greatly enhanced after ICA. ► Our test statistic is sensitive to both, missing components and changes in SNR.</description><identifier>ISSN: 1053-8119</identifier><identifier>EISSN: 1095-9572</identifier><identifier>DOI: 10.1016/j.neuroimage.2011.08.030</identifier><identifier>PMID: 21875673</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Algorithms ; Artificial Intelligence ; Brain ; Brain - cytology ; Cameras ; Digitization ; Fiber tracking ; Human connectome ; Humans ; ICA ; Identification ; Image Enhancement - methods ; Image Interpretation, Computer-Assisted - methods ; Independent component analysis ; Light ; Lighting - methods ; Microscopy, Polarization - methods ; Nerve Fibers, Myelinated - ultrastructure ; Neurons - cytology ; Noise ; Pattern Recognition, Automated - methods ; PLI ; Polarized light imaging ; Reproducibility of Results ; Sensitivity and Specificity ; Software</subject><ispartof>NeuroImage (Orlando, Fla.), 2012-01, Vol.59 (2), p.1338-1347</ispartof><rights>2011 Elsevier Inc.</rights><rights>Copyright © 2011 Elsevier Inc. All rights reserved.</rights><rights>Copyright Elsevier Limited Jan 16, 2012</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c499t-65f0762895600c5955def961c0bcd74fd31ddd548b1279d019ede569a947df503</citedby><cites>FETCH-LOGICAL-c499t-65f0762895600c5955def961c0bcd74fd31ddd548b1279d019ede569a947df503</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.proquest.com/docview/1877801127?pq-origsite=primo$$EHTML$$P50$$Gproquest$$H</linktohtml><link.rule.ids>315,782,786,3552,27931,27932,46002,64392,64394,64396,72476</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21875673$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dammers, Jürgen</creatorcontrib><creatorcontrib>Breuer, Lukas</creatorcontrib><creatorcontrib>Axer, Markus</creatorcontrib><creatorcontrib>Kleiner, Melanie</creatorcontrib><creatorcontrib>Eiben, Björn</creatorcontrib><creatorcontrib>Gräßel, David</creatorcontrib><creatorcontrib>Dickscheid, Timo</creatorcontrib><creatorcontrib>Zilles, Karl</creatorcontrib><creatorcontrib>Amunts, Katrin</creatorcontrib><creatorcontrib>Shah, N. Joni</creatorcontrib><creatorcontrib>Pietrzyk, Uwe</creatorcontrib><title>Automatic identification of gray and white matter components in polarized light imaging</title><title>NeuroImage (Orlando, Fla.)</title><addtitle>Neuroimage</addtitle><description>Polarized light imaging (PLI) enables the visualization of fiber tracts with high spatial resolution in microtome sections of postmortem brains. Vectors of the fiber orientation defined by inclination and direction angles can directly be derived from the optical signals employed by PLI analysis. The polarization state of light propagating through a rotating polarimeter is varied in such a way that the detected signal of each spatial unit describes a sinusoidal signal. Noise, light scatter and filter inhomogeneities, however, interfere with the original sinusoidal PLI signals, which in turn have direct impact on the accuracy of subsequent fiber tracking. Recently we showed that the primary sinusoidal signals can effectively be restored after noise and artifact rejection utilizing independent component analysis (ICA). In particular, regions with weak intensities are greatly enhanced after ICA based artifact rejection and signal restoration.
Here, we propose a user independent way of identifying the components of interest after decomposition; i.e., components that are related to gray and white matter. Depending on the size of the postmortem brain and the section thickness, the number of independent component maps can easily be in the range of a few ten thousand components for one brain. Therefore, we developed an automatic and, more importantly, user independent way of extracting the signal of interest. The automatic identification of gray and white matter components is based on the evaluation of the statistical properties of the so-called feature vectors of each individual component map, which, in the ideal case, shows a sinusoidal waveform. Our method enables large-scale analysis (i.e., the analysis of thousands of whole brain sections) of nerve fiber orientations in the human brain using polarized light imaging.
► Novel approach to automatically identify gray and white matter components from PLI. ► User independent way of signal enhancement in a large set of PLI images. ► The method includes artifact and noise rejection utilizing ICA. ► Regions with weak intensities are greatly enhanced after ICA. ► Our test statistic is sensitive to both, missing components and changes in SNR.</description><subject>Algorithms</subject><subject>Artificial Intelligence</subject><subject>Brain</subject><subject>Brain - cytology</subject><subject>Cameras</subject><subject>Digitization</subject><subject>Fiber tracking</subject><subject>Human connectome</subject><subject>Humans</subject><subject>ICA</subject><subject>Identification</subject><subject>Image Enhancement - methods</subject><subject>Image Interpretation, Computer-Assisted - methods</subject><subject>Independent component analysis</subject><subject>Light</subject><subject>Lighting - methods</subject><subject>Microscopy, Polarization - methods</subject><subject>Nerve Fibers, Myelinated - ultrastructure</subject><subject>Neurons - cytology</subject><subject>Noise</subject><subject>Pattern Recognition, Automated - methods</subject><subject>PLI</subject><subject>Polarized light imaging</subject><subject>Reproducibility of Results</subject><subject>Sensitivity and Specificity</subject><subject>Software</subject><issn>1053-8119</issn><issn>1095-9572</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkUtv1DAUhS1ERR_wF5AlFqwSrpP4tSwVj0qV2FCxtDL2zdSjxJ7aDqj8ejyaQiU2sLItfdfnnnMIoQxaBky827UB1xT9Mm6x7YCxFlQLPTwjZww0bzSX3fPDnfeNYkyfkvOcdwCg2aBekNOOKcmF7M_It8u1xGUs3lLvMBQ_eVtfMdA40W0aH-gYHP1x5wvSihVM1MZlH0NlM_WB7uM8Jv8THZ399q7Qw04-bF-Sk2mcM756PC_I7ccPX68-NzdfPl1fXd40dtC6NIJPIEWnNBcAlmvOHU5aMAsb6-QwuZ455_igNqyT2gHT6JALPepBuolDf0HeHv_dp3i_Yi5m8dniPI8B45qNZqJa7jrxH2SV6TmoSr75i9zFNYVqw9TcpKp5d7JS6kjZFHNOOJl9qubTg2FgDi2ZnXlqyRxaMqBMbamOvn4UWDcLuj-Dv2upwPsjgDW67x6TydZjsOh8QluMi_7fKr8AzqaoOQ</recordid><startdate>20120116</startdate><enddate>20120116</enddate><creator>Dammers, Jürgen</creator><creator>Breuer, Lukas</creator><creator>Axer, Markus</creator><creator>Kleiner, Melanie</creator><creator>Eiben, Björn</creator><creator>Gräßel, David</creator><creator>Dickscheid, Timo</creator><creator>Zilles, Karl</creator><creator>Amunts, Katrin</creator><creator>Shah, N. 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Joni</au><au>Pietrzyk, Uwe</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Automatic identification of gray and white matter components in polarized light imaging</atitle><jtitle>NeuroImage (Orlando, Fla.)</jtitle><addtitle>Neuroimage</addtitle><date>2012-01-16</date><risdate>2012</risdate><volume>59</volume><issue>2</issue><spage>1338</spage><epage>1347</epage><pages>1338-1347</pages><issn>1053-8119</issn><eissn>1095-9572</eissn><abstract>Polarized light imaging (PLI) enables the visualization of fiber tracts with high spatial resolution in microtome sections of postmortem brains. Vectors of the fiber orientation defined by inclination and direction angles can directly be derived from the optical signals employed by PLI analysis. The polarization state of light propagating through a rotating polarimeter is varied in such a way that the detected signal of each spatial unit describes a sinusoidal signal. Noise, light scatter and filter inhomogeneities, however, interfere with the original sinusoidal PLI signals, which in turn have direct impact on the accuracy of subsequent fiber tracking. Recently we showed that the primary sinusoidal signals can effectively be restored after noise and artifact rejection utilizing independent component analysis (ICA). In particular, regions with weak intensities are greatly enhanced after ICA based artifact rejection and signal restoration.
Here, we propose a user independent way of identifying the components of interest after decomposition; i.e., components that are related to gray and white matter. Depending on the size of the postmortem brain and the section thickness, the number of independent component maps can easily be in the range of a few ten thousand components for one brain. Therefore, we developed an automatic and, more importantly, user independent way of extracting the signal of interest. The automatic identification of gray and white matter components is based on the evaluation of the statistical properties of the so-called feature vectors of each individual component map, which, in the ideal case, shows a sinusoidal waveform. Our method enables large-scale analysis (i.e., the analysis of thousands of whole brain sections) of nerve fiber orientations in the human brain using polarized light imaging.
► Novel approach to automatically identify gray and white matter components from PLI. ► User independent way of signal enhancement in a large set of PLI images. ► The method includes artifact and noise rejection utilizing ICA. ► Regions with weak intensities are greatly enhanced after ICA. ► Our test statistic is sensitive to both, missing components and changes in SNR.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>21875673</pmid><doi>10.1016/j.neuroimage.2011.08.030</doi><tpages>10</tpages></addata></record> |
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subjects | Algorithms Artificial Intelligence Brain Brain - cytology Cameras Digitization Fiber tracking Human connectome Humans ICA Identification Image Enhancement - methods Image Interpretation, Computer-Assisted - methods Independent component analysis Light Lighting - methods Microscopy, Polarization - methods Nerve Fibers, Myelinated - ultrastructure Neurons - cytology Noise Pattern Recognition, Automated - methods PLI Polarized light imaging Reproducibility of Results Sensitivity and Specificity Software |
title | Automatic identification of gray and white matter components in polarized light imaging |
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