Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images

Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bi...
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Autor*in:	Ali Daraei [verfasserIn] Marlien Pieters [verfasserIn] Stephen R. Baker [verfasserIn] Zelda de Lange-Loots [verfasserIn] Aleksander Siniarski [verfasserIn] Rustem I. Litvinov [verfasserIn] Caroline S. B. Veen [verfasserIn] Moniek P. M. de Maat [verfasserIn] John W. Weisel [verfasserIn] Robert A. S. Ariëns [verfasserIn] Martin Guthold [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	automated analysis DiameterJ structure fibrin fibers plasma clots diameter

Übergeordnetes Werk:	In: Biomolecules - MDPI AG, 2013, 11(2021), 10, p 1536
Übergeordnetes Werk:	volume:11 ; year:2021 ; number:10, p 1536

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/biom11101536

Katalog-ID:	DOAJ016652320

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520			\|a Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). Determining fibrin clot porosity via DiameterJ is challenging.
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allfields	10.3390/biom11101536 doi (DE-627)DOAJ016652320 (DE-599)DOAJdd8dd48477f94d0a8ce5e81e78213674 DE-627 ger DE-627 rakwb eng QR1-502 Ali Daraei verfasserin aut Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). Determining fibrin clot porosity via DiameterJ is challenging. automated analysis DiameterJ structure fibrin fibers plasma clots diameter Microbiology Marlien Pieters verfasserin aut Stephen R. Baker verfasserin aut Zelda de Lange-Loots verfasserin aut Aleksander Siniarski verfasserin aut Rustem I. Litvinov verfasserin aut Caroline S. B. Veen verfasserin aut Moniek P. M. de Maat verfasserin aut John W. Weisel verfasserin aut Robert A. S. Ariëns verfasserin aut Martin Guthold verfasserin aut In Biomolecules MDPI AG, 2013 11(2021), 10, p 1536 (DE-627)735688915 (DE-600)2701262-1 2218273X nnns volume:11 year:2021 number:10, p 1536 https://doi.org/10.3390/biom11101536 kostenfrei https://doaj.org/article/dd8dd48477f94d0a8ce5e81e78213674 kostenfrei https://www.mdpi.com/2218-273X/11/10/1536 kostenfrei https://doaj.org/toc/2218-273X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2021 10, p 1536
spelling	10.3390/biom11101536 doi (DE-627)DOAJ016652320 (DE-599)DOAJdd8dd48477f94d0a8ce5e81e78213674 DE-627 ger DE-627 rakwb eng QR1-502 Ali Daraei verfasserin aut Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). Determining fibrin clot porosity via DiameterJ is challenging. automated analysis DiameterJ structure fibrin fibers plasma clots diameter Microbiology Marlien Pieters verfasserin aut Stephen R. Baker verfasserin aut Zelda de Lange-Loots verfasserin aut Aleksander Siniarski verfasserin aut Rustem I. Litvinov verfasserin aut Caroline S. B. Veen verfasserin aut Moniek P. M. de Maat verfasserin aut John W. Weisel verfasserin aut Robert A. S. Ariëns verfasserin aut Martin Guthold verfasserin aut In Biomolecules MDPI AG, 2013 11(2021), 10, p 1536 (DE-627)735688915 (DE-600)2701262-1 2218273X nnns volume:11 year:2021 number:10, p 1536 https://doi.org/10.3390/biom11101536 kostenfrei https://doaj.org/article/dd8dd48477f94d0a8ce5e81e78213674 kostenfrei https://www.mdpi.com/2218-273X/11/10/1536 kostenfrei https://doaj.org/toc/2218-273X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2021 10, p 1536
allfields_unstemmed	10.3390/biom11101536 doi (DE-627)DOAJ016652320 (DE-599)DOAJdd8dd48477f94d0a8ce5e81e78213674 DE-627 ger DE-627 rakwb eng QR1-502 Ali Daraei verfasserin aut Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). Determining fibrin clot porosity via DiameterJ is challenging. automated analysis DiameterJ structure fibrin fibers plasma clots diameter Microbiology Marlien Pieters verfasserin aut Stephen R. Baker verfasserin aut Zelda de Lange-Loots verfasserin aut Aleksander Siniarski verfasserin aut Rustem I. Litvinov verfasserin aut Caroline S. B. Veen verfasserin aut Moniek P. M. de Maat verfasserin aut John W. Weisel verfasserin aut Robert A. S. Ariëns verfasserin aut Martin Guthold verfasserin aut In Biomolecules MDPI AG, 2013 11(2021), 10, p 1536 (DE-627)735688915 (DE-600)2701262-1 2218273X nnns volume:11 year:2021 number:10, p 1536 https://doi.org/10.3390/biom11101536 kostenfrei https://doaj.org/article/dd8dd48477f94d0a8ce5e81e78213674 kostenfrei https://www.mdpi.com/2218-273X/11/10/1536 kostenfrei https://doaj.org/toc/2218-273X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2021 10, p 1536
allfieldsGer	10.3390/biom11101536 doi (DE-627)DOAJ016652320 (DE-599)DOAJdd8dd48477f94d0a8ce5e81e78213674 DE-627 ger DE-627 rakwb eng QR1-502 Ali Daraei verfasserin aut Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). Determining fibrin clot porosity via DiameterJ is challenging. automated analysis DiameterJ structure fibrin fibers plasma clots diameter Microbiology Marlien Pieters verfasserin aut Stephen R. Baker verfasserin aut Zelda de Lange-Loots verfasserin aut Aleksander Siniarski verfasserin aut Rustem I. Litvinov verfasserin aut Caroline S. B. Veen verfasserin aut Moniek P. M. de Maat verfasserin aut John W. Weisel verfasserin aut Robert A. S. Ariëns verfasserin aut Martin Guthold verfasserin aut In Biomolecules MDPI AG, 2013 11(2021), 10, p 1536 (DE-627)735688915 (DE-600)2701262-1 2218273X nnns volume:11 year:2021 number:10, p 1536 https://doi.org/10.3390/biom11101536 kostenfrei https://doaj.org/article/dd8dd48477f94d0a8ce5e81e78213674 kostenfrei https://www.mdpi.com/2218-273X/11/10/1536 kostenfrei https://doaj.org/toc/2218-273X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2021 10, p 1536
allfieldsSound	10.3390/biom11101536 doi (DE-627)DOAJ016652320 (DE-599)DOAJdd8dd48477f94d0a8ce5e81e78213674 DE-627 ger DE-627 rakwb eng QR1-502 Ali Daraei verfasserin aut Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). Determining fibrin clot porosity via DiameterJ is challenging. automated analysis DiameterJ structure fibrin fibers plasma clots diameter Microbiology Marlien Pieters verfasserin aut Stephen R. Baker verfasserin aut Zelda de Lange-Loots verfasserin aut Aleksander Siniarski verfasserin aut Rustem I. Litvinov verfasserin aut Caroline S. B. Veen verfasserin aut Moniek P. M. de Maat verfasserin aut John W. Weisel verfasserin aut Robert A. S. Ariëns verfasserin aut Martin Guthold verfasserin aut In Biomolecules MDPI AG, 2013 11(2021), 10, p 1536 (DE-627)735688915 (DE-600)2701262-1 2218273X nnns volume:11 year:2021 number:10, p 1536 https://doi.org/10.3390/biom11101536 kostenfrei https://doaj.org/article/dd8dd48477f94d0a8ce5e81e78213674 kostenfrei https://www.mdpi.com/2218-273X/11/10/1536 kostenfrei https://doaj.org/toc/2218-273X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2021 10, p 1536
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callnumber-first	Q - Science
author	Ali Daraei
spellingShingle	Ali Daraei misc QR1-502 misc automated analysis misc DiameterJ misc structure misc fibrin fibers misc plasma clots misc diameter misc Microbiology Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images
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topic_title	QR1-502 Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images automated analysis DiameterJ structure fibrin fibers plasma clots diameter
topic	misc QR1-502 misc automated analysis misc DiameterJ misc structure misc fibrin fibers misc plasma clots misc diameter misc Microbiology
topic_unstemmed	misc QR1-502 misc automated analysis misc DiameterJ misc structure misc fibrin fibers misc plasma clots misc diameter misc Microbiology
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title	Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images
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title_full	Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images
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author_browse	Ali Daraei Marlien Pieters Stephen R. Baker Zelda de Lange-Loots Aleksander Siniarski Rustem I. Litvinov Caroline S. B. Veen Moniek P. M. de Maat John W. Weisel Robert A. S. Ariëns Martin Guthold
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title_sort	automated fiber diameter and porosity measurements of plasma clots in scanning electron microscopy images
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title_auth	Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images
abstract	Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). Determining fibrin clot porosity via DiameterJ is challenging.
abstractGer	Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). Determining fibrin clot porosity via DiameterJ is challenging.
abstract_unstemmed	Scanning Electron Microscopy (SEM) is a powerful, high-resolution imaging technique widely used to analyze the structure of fibrin networks. Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). Determining fibrin clot porosity via DiameterJ is challenging.
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title_short	Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images
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Currently, structural features, such as fiber diameter, length, density, and porosity, are mostly analyzed manually, which is tedious and may introduce user bias. A reliable, automated structural image analysis method would mitigate these drawbacks. We evaluated the performance of DiameterJ (an ImageJ plug-in) for analyzing fibrin fiber diameter by comparing automated DiameterJ outputs with manual diameter measurements in four SEM data sets with different imaging parameters. We also investigated correlations between biophysical fibrin clot properties and diameter, and between clot permeability and DiameterJ-determined clot porosity. Several of the 24 DiameterJ algorithms returned diameter values that highly correlated with and closely matched the values of the manual measurements. However, optimal performance was dependent on the pixel size of the images—best results were obtained for images with a pixel size of 8–10 nm (13–16 pixels/fiber). Larger or smaller pixels resulted in an over- or underestimation of diameter values, respectively. The correlation between clot permeability and DiameterJ-determined clot porosity was modest, likely because it is difficult to establish the correct image depth of field in this analysis. In conclusion, several DiameterJ algorithms (M6, M5, T3) perform well for diameter determination from SEM images, given the appropriate imaging conditions (13–16 pixels/fiber). 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Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images

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