{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/105215"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/105215","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Computational tools for monitoring neural connectivity using calcium imaging","abstract":"The development of optogenetics and calcium imaging have enabled light-activated manipulation and monitoring of neural activity that offer powerful alternatives to traditional electronic and chemical methods. Along with light-evoked activity, many technical advancements have been made that allow for facilitated optical delivery, activation, and recording of neural dynamics. These include fiber-optic cables for targeted optical delivery, genetically encoded calcium indicators (GECI) for optically measuring signaling dynamics, fiber bundles for spatially targeted delivery, and optical system design for adequate integration of these technologies. Recently, this field has grown substantially, with the goal to understand neural communication based on signals transmitted between cells that lead to brain-level function. In addition to optical and genetic advancements, equally important are methods for assessing both single-cell and network-level behavior. With high volumes of data from video-rate optical imaging and stimulation systems, comes the challenge of analyzing their trends. This is especially true for inferring network-level behavior, given the limited field-of-view inherent in optical systems. In addition, when using fiber bundles, either for in vitro or in vivo experiments, there are inherent artifacts that obscure the underlying imagery, hindering data interpretation and analysis. The goal of this thesis is twofold: to present an algorithm developed for assessing network dynamics from calcium imaging data, and an algorithm aimed at removing the pixilation artifact from fiber-bundle images. The neural connectivity algorithm could be used to reveal connectivity between neurons. Furthermore, a map of connectivity in neural cultures could be developed to showcase the network structure in neural preparations. By integrating these into optical systems, underlying network behavior can be identified and better understood, and directed electromagnetic manipulation of neural circuits can be realized. These algorithms, coupled with all-optical approaches to assess network dynamics, provide a powerful tool that when fully integrated, will allow for closed-loop optogenetic feedback mechanisms in brain cultures, slices, and retinal samples to potentially evoke known and desired responses.","abstract_html":"The development of optogenetics and calcium imaging have enabled light-activated manipulation and monitoring of neural activity that offer powerful alternatives to traditional electronic and chemical methods. Along with light-evoked activity, many technical advancements have been made that allow for facilitated optical delivery, activation, and recording of neural dynamics. These include fiber-optic cables for targeted optical delivery, genetically encoded calcium indicators (GECI) for optically measuring signaling dynamics, fiber bundles for spatially targeted delivery, and optical system design for adequate integration of these technologies. Recently, this field has grown substantially, with the goal to understand neural communication based on signals transmitted between cells that lead to brain-level function. In addition to optical and genetic advancements, equally important are methods for assessing both single-cell and network-level behavior. With high volumes of data from video-rate optical imaging and stimulation systems, comes the challenge of analyzing their trends. This is especially true for inferring network-level behavior, given the limited field-of-view inherent in optical systems. In addition, when using fiber bundles, either for in vitro or in vivo experiments, there are inherent artifacts that obscure the underlying imagery, hindering data interpretation and analysis. The goal of this thesis is twofold: to present an algorithm developed for assessing network dynamics from calcium imaging data, and an algorithm aimed at removing the pixilation artifact from fiber-bundle images. The neural connectivity algorithm could be used to reveal connectivity between neurons. Furthermore, a map of connectivity in neural cultures could be developed to showcase the network structure in neural preparations. By integrating these into optical systems, underlying network behavior can be identified and better understood, and directed electromagnetic manipulation of neural circuits can be realized. These algorithms, coupled with all-optical approaches to assess network dynamics, provide a powerful tool that when fully integrated, will allow for closed-loop optogenetic feedback mechanisms in brain cultures, slices, and retinal samples to potentially evoke known and desired responses.","abstract_has_math":false,"creators":["Renteria, Carlos"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Bioengineering","degree_department":null,"school":null,"contributors":["Boppart, Stephen A."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019-08-23T20:47:33Z","date_published":"2019-08-23T20:47:33Z","updated_at":"2026-07-22T22:24:44Z","subjects":["Calcium imaging","Neuron","Connectivity","Fiber bundle"],"languages":["en"],"rights":["Copyright 2019 Carlos Renteria"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/105215","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Boppart, Stephen A."]},{"key":"dc:creator","label":"Author","values":["Renteria, Carlos"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2019-08-23T20:47:33Z","2021-08-24T09:15:16Z","2019-04-17","2019-05"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Bioengineering"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Calcium imaging","Neuron","Connectivity","Fiber bundle"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2019 Carlos Renteria"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/105215"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The development of optogenetics and calcium imaging have enabled light-activated manipulation and monitoring of neural activity that offer powerful alternatives to traditional electronic and chemical methods. Along with light-evoked activity, many technical advancements have been made that allow for facilitated optical delivery, activation, and recording of neural dynamics. These include fiber-optic cables for targeted optical delivery, genetically encoded calcium indicators (GECI) for optically measuring signaling dynamics, fiber bundles for spatially targeted delivery, and optical system design for adequate integration of these technologies. Recently, this field has grown substantially, with the goal to understand neural communication based on signals transmitted between cells that lead to brain-level function. In addition to optical and genetic advancements, equally important are methods for assessing both single-cell and network-level behavior. With high volumes of data from video-rate optical imaging and stimulation systems, comes the challenge of analyzing their trends. This is especially true for inferring network-level behavior, given the limited field-of-view inherent in optical systems. In addition, when using fiber bundles, either for in vitro or in vivo experiments, there are inherent artifacts that obscure the underlying imagery, hindering data interpretation and analysis. The goal of this thesis is twofold: to present an algorithm developed for assessing network dynamics from calcium imaging data, and an algorithm aimed at removing the pixilation artifact from fiber-bundle images. The neural connectivity algorithm could be used to reveal connectivity between neurons. Furthermore, a map of connectivity in neural cultures could be developed to showcase the network structure in neural preparations. By integrating these into optical systems, underlying network behavior can be identified and better understood, and directed electromagnetic manipulation of neural circuits can be realized. These algorithms, coupled with all-optical approaches to assess network dynamics, provide a powerful tool that when fully integrated, will allow for closed-loop optogenetic feedback mechanisms in brain cultures, slices, and retinal samples to potentially evoke known and desired responses.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-05-01","The student, Carlos Renteria, accepted the attached license on 2019-04-17 at 12:16.","The student, Carlos Renteria, submitted this Thesis for approval on 2019-04-17 at 12:19.","This Thesis was approved for publication on 2019-04-17 at 20:05.","DSpace SAF Submission Ingestion Package generated from Vireo submission #13713 on 2019-08-22 at 16:23:03","Made available in DSpace on 2019-08-23T20:47:33Z (GMT). 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Along with light-evoked activity, many technical advancements have been made that allow for facilitated optical delivery, activation, and recording of neural dynamics. These include fiber-optic cables for targeted optical delivery, genetically encoded calcium indicators (GECI) for optically measuring signaling dynamics, fiber bundles for spatially targeted delivery, and optical system design for adequate integration of these technologies. Recently, this field has grown substantially, with the goal to understand neural communication based on signals transmitted between cells that lead to brain-level function. In addition to optical and genetic advancements, equally important are methods for assessing both single-cell and network-level behavior. With high volumes of data from video-rate optical imaging and stimulation systems, comes the challenge of analyzing their trends. This is especially true for inferring network-level behavior, given the limited field-of-view inherent in optical systems. In addition, when using fiber bundles, either for in vitro or in vivo experiments, there are inherent artifacts that obscure the underlying imagery, hindering data interpretation and analysis. The goal of this thesis is twofold: to present an algorithm developed for assessing network dynamics from calcium imaging data, and an algorithm aimed at removing the pixilation artifact from fiber-bundle images. The neural connectivity algorithm could be used to reveal connectivity between neurons. Furthermore, a map of connectivity in neural cultures could be developed to showcase the network structure in neural preparations. By integrating these into optical systems, underlying network behavior can be identified and better understood, and directed electromagnetic manipulation of neural circuits can be realized. These algorithms, coupled with all-optical approaches to assess network dynamics, provide a powerful tool that when fully integrated, will allow for closed-loop optogenetic feedback mechanisms in brain cultures, slices, and retinal samples to potentially evoke known and desired responses.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-05-01","The student, Carlos Renteria, accepted the attached license on 2019-04-17 at 12:16.","The student, Carlos Renteria, submitted this Thesis for approval on 2019-04-17 at 12:19.","This Thesis was approved for publication on 2019-04-17 at 20:05.","DSpace SAF Submission Ingestion Package generated from Vireo submission #13713 on 2019-08-22 at 16:23:03","Made available in DSpace on 2019-08-23T20:47:33Z (GMT). No. of bitstreams: 2 RENTERIA-THESIS-2019.pdf: 5667539 bytes, checksum: 566e6d11c35120e7de18a0a4d2208101 (MD5) LICENSE.txt: 4212 bytes, checksum: db2c543b5797e0f6f9facdb09179e21a (MD5) Previous issue date: 2019-04-17","Embargo set by: Seth Robbins for item 112336 Lift date: 2021-08-23T20:47:38Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 112336 Lift date: 2021-08-23T20:48:32Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 112336 on 2021-08-24T09:15:16Z."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/105215"],"dc:language":["en"],"dc:rights":["Copyright 2019 Carlos Renteria"],"dc:subject":["Calcium imaging","Neuron","Connectivity","Fiber bundle"],"dc:title":["Computational tools for monitoring neural connectivity using calcium imaging"],"dc:type":["text"],"thesis:degree_discipline":["Bioengineering"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:44Z"}