Three-dimensional reconstructions of marine fine-grained sediment open a new dimension for studying nano- and microscale organo-clay fabric important to improving and advancing organic matter (OM) sequestration and fluid flow dynamics modeling. I created 3-D reconstructions of clay fabric and pore pathways from serial sections and photographic mosaics obtained using transmission electron microscopy. These reconstructions show aggregations of clay domains, surrounding OM, and pore networks. I examined a Model sample (laboratory consolidated) with 1% OM and a Natural sample (polychaete fecal pellet) with high levels of OM. Three-dimensional reconstructions were segmented into 300 nm cube subsamples to make highly localized qualitative observations and quantitative measurements of porosity, particle and pore orientation and volume, and pore network tortuosity.
Flow pathway spreadsheet maps were created based on pore size and orientation. This technique allows tortuosity to be calculated for 3-D reconstructions while restricting porosity to a minimum boundary condition prior to determining tortuous pathways. Measurements of 2-D photographs and 3-D reconstructions using the same serial photographs showed that pathlengths measured for tortuosity were for the most part statistically similar. The range of porosities and the number of pathways through which flow could pass through the sample are significantly higher in 3-D analyses. Thus, measurements made from 2-D sediment pathway studies provide limited information, omitting a significant number of diffusion and flow pathways that cannot be resolved in two dimensions.
","abstract_html":"<p>Three-dimensional reconstructions of marine fine-grained sediment open a new dimension for studying nano- and microscale organo-clay fabric important to improving and advancing organic matter (OM) sequestration and fluid flow dynamics modeling. I created 3-D reconstructions of clay fabric and pore pathways from serial sections and photographic mosaics obtained using transmission electron microscopy. These reconstructions show aggregations of clay domains, surrounding OM, and pore networks. I examined a Model sample (laboratory consolidated) with 1% OM and a Natural sample (polychaete fecal pellet) with high levels of OM. Three-dimensional reconstructions were segmented into 300 nm cube subsamples to make highly localized qualitative observations and quantitative measurements of porosity, particle and pore orientation and volume, and pore network tortuosity.</p> <p>Flow pathway spreadsheet maps were created based on pore size and orientation. This technique allows tortuosity to be calculated for 3-D reconstructions while restricting porosity to a minimum boundary condition prior to determining tortuous pathways. Measurements of 2-D photographs and 3-D reconstructions using the same serial photographs showed that pathlengths measured for tortuosity were for the most part statistically similar. The range of porosities and the number of pathways through which flow could pass through the sample are significantly higher in 3-D analyses. Thus, measurements made from 2-D sediment pathway studies provide limited information, omitting a significant number of diffusion and flow pathways that cannot be resolved in two dimensions.</p>","abstract_has_math":false,"creators":["Douglas, Jessica Rae Gardner"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Masters Thesis","degree_discipline":"Biological Sciences","degree_department":null,"school":null,"contributors":["Kenneth J. Curry","Richard H. Bennett","Franklin T. Heitmuller"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-05-01T07:00:00Z","date_published":"2014-05-01T07:00:00Z","updated_at":"2026-07-24T05:44:27Z","subjects":["clay fabric","3-D reconstruction","transmission electron microscopy","pore network","nanometer scale","marine sediment","Biology","Earth Sciences","Life Sciences","Physical Sciences and Mathematics","Sedimentology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://aquila.usm.edu/masters_theses/7","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Kenneth J. Curry","Richard H. Bennett","Franklin T. Heitmuller"]},{"key":"dc:creator","label":"Author","values":["Douglas, Jessica Rae Gardner"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2014-06-20T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biological Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Masters Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["clay fabric","3-D reconstruction","transmission electron microscopy","pore network","nanometer scale","marine sediment","Biology","Earth Sciences","Life Sciences","Physical Sciences and Mathematics","Sedimentology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://aquila.usm.edu/masters_theses/7"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Three-dimensional reconstructions of marine fine-grained sediment open a new dimension for studying nano- and microscale organo-clay fabric important to improving and advancing organic matter (OM) sequestration and fluid flow dynamics modeling. I created 3-D reconstructions of clay fabric and pore pathways from serial sections and photographic mosaics obtained using transmission electron microscopy. These reconstructions show aggregations of clay domains, surrounding OM, and pore networks. I examined a Model sample (laboratory consolidated) with 1% OM and a Natural sample (polychaete fecal pellet) with high levels of OM. Three-dimensional reconstructions were segmented into 300 nm cube subsamples to make highly localized qualitative observations and quantitative measurements of porosity, particle and pore orientation and volume, and pore network tortuosity.
Flow pathway spreadsheet maps were created based on pore size and orientation. This technique allows tortuosity to be calculated for 3-D reconstructions while restricting porosity to a minimum boundary condition prior to determining tortuous pathways. Measurements of 2-D photographs and 3-D reconstructions using the same serial photographs showed that pathlengths measured for tortuosity were for the most part statistically similar. The range of porosities and the number of pathways through which flow could pass through the sample are significantly higher in 3-D analyses. Thus, measurements made from 2-D sediment pathway studies provide limited information, omitting a significant number of diffusion and flow pathways that cannot be resolved in two dimensions.
"]},{"key":"dc:title","label":"Title","values":["Three-Dimensional Reconstruction of Marine Clay Nano- and Microstructure By Transmission Electron Microscopy: Analysis of Fabric and Pore Network"]}]}],"canonical_facts":{"dc:contributor":["Kenneth J. Curry","Richard H. Bennett","Franklin T. Heitmuller"],"dc:creator":["Douglas, Jessica Rae Gardner"],"dc:date.available":["2014-06-20T07:00:00Z"],"dc:description.abstract":["Three-dimensional reconstructions of marine fine-grained sediment open a new dimension for studying nano- and microscale organo-clay fabric important to improving and advancing organic matter (OM) sequestration and fluid flow dynamics modeling. I created 3-D reconstructions of clay fabric and pore pathways from serial sections and photographic mosaics obtained using transmission electron microscopy. These reconstructions show aggregations of clay domains, surrounding OM, and pore networks. I examined a Model sample (laboratory consolidated) with 1% OM and a Natural sample (polychaete fecal pellet) with high levels of OM. Three-dimensional reconstructions were segmented into 300 nm cube subsamples to make highly localized qualitative observations and quantitative measurements of porosity, particle and pore orientation and volume, and pore network tortuosity.
Flow pathway spreadsheet maps were created based on pore size and orientation. This technique allows tortuosity to be calculated for 3-D reconstructions while restricting porosity to a minimum boundary condition prior to determining tortuous pathways. Measurements of 2-D photographs and 3-D reconstructions using the same serial photographs showed that pathlengths measured for tortuosity were for the most part statistically similar. The range of porosities and the number of pathways through which flow could pass through the sample are significantly higher in 3-D analyses. Thus, measurements made from 2-D sediment pathway studies provide limited information, omitting a significant number of diffusion and flow pathways that cannot be resolved in two dimensions.
"],"dc:identifier":["https://aquila.usm.edu/masters_theses/7"],"dc:subject":["clay fabric","3-D reconstruction","transmission electron microscopy","pore network","nanometer scale","marine sediment","Biology","Earth Sciences","Life Sciences","Physical Sciences and Mathematics","Sedimentology"],"dc:title":["Three-Dimensional Reconstruction of Marine Clay Nano- and Microstructure By Transmission Electron Microscopy: Analysis of Fabric and Pore Network"],"thesis:degree_discipline":["Biological Sciences"],"thesis:degree_level":["Masters Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T05:44:27Z"}