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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/11/10/1536 |
| _version_ | 1797515179653595136 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Ali Daraei |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T06:42:50Z |
| format | Article |
| id | doaj.art-dd8dd48477f94d0a8ce5e81e78213674 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T06:42:50Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-dd8dd48477f94d0a8ce5e81e782136742023-11-22T17:35:08ZengMDPI AGBiomolecules2218-273X2021-10-011110153610.3390/biom11101536Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy ImagesAli Daraei0Marlien Pieters1Stephen R. Baker2Zelda de Lange-Loots3Aleksander Siniarski4Rustem I. Litvinov5Caroline S. B. Veen6Moniek P. M. de Maat7John W. Weisel8Robert A. S. Ariëns9Martin Guthold10Department of Physics, Wake Forest University, Winston-Salem, NC 27109, USACenter of Excellence for Nutrition (CEN), Potchefstroom Campus, North-West University, Potchefstroom 2520, South AfricaDepartment of Physics, Wake Forest University, Winston-Salem, NC 27109, USACenter of Excellence for Nutrition (CEN), Potchefstroom Campus, North-West University, Potchefstroom 2520, South AfricaDepartment of Coronary Disease and Heart Failure, Institute of Cardiology, Jagiellonian University Medical College, 31-202 Krakow, PolandDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USADepartment of Hematology, Erasmus University Medical Center, 3015 GD Rotterdam, The NetherlandsDepartment of Hematology, Erasmus University Medical Center, 3015 GD Rotterdam, The NetherlandsDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USALeeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS16 8FX, UKDepartment of Physics, Wake Forest University, Winston-Salem, NC 27109, USAScanning 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.https://www.mdpi.com/2218-273X/11/10/1536automated analysisDiameterJstructurefibrin fibersplasma clotsdiameter |
| spellingShingle | 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 Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images Biomolecules automated analysis DiameterJ structure fibrin fibers plasma clots diameter |
| title | Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images |
| title_full | Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images |
| title_fullStr | Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images |
| title_full_unstemmed | Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images |
| title_short | Automated Fiber Diameter and Porosity Measurements of Plasma Clots in Scanning Electron Microscopy Images |
| title_sort | automated fiber diameter and porosity measurements of plasma clots in scanning electron microscopy images |
| topic | automated analysis DiameterJ structure fibrin fibers plasma clots diameter |
| url | https://www.mdpi.com/2218-273X/11/10/1536 |
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