{"id":{"repo_id":"uic","oai_identifier":"oai:figshare.com:article/32993807"},"canonical_url":"https://search.dev.ndltd.org/etd/uic/oai:figshare.com:article/32993807","repository":{"repo_id":"uic","name":"University of Illinois - Chicago","base_url":"https://api.figshare.com/v2/oai"},"display":{"title":"Modular, Open-Source Instrumentation for Zebrafish Larvae Research","abstract":"Access to experimental infrastructure remains a major limiting factor in biological research, particularly in behavioral neuroscience and genetic engineering, where many widely used tools are proprietary, expensive, and closed by design. This thesis demonstrates that recent advances in desktop 3D printing and free and open-source software have reached a level of maturity that allows many proprietary research tools to be replaced with open, low-cost alternatives that meet the functional requirements of commercial systems while remaining modifiable, transparent, and affordable. The work presents the OpenZebra toolset, a collection of open hardware and software platforms designed to support zebrafish larvae research. The Agarose Stamping Device provides reproducible larval immobilization with high positional repeatability, replacing fragile manual techniques with a standardized process that can be fabricated, modified, and shared without specialized manufacturing infrastructure. The Zebrafish Larva Interface extends this foundation by integrating 3D-printed mechanical components, commodity imaging hardware, and open-source software to enable quantitative optokinetic response measurements and closed-loop interaction between larval behavior and external systems. Application to pharmacological perturbation studies demonstrates the platform's sensitivity and adaptability, while the OpenZebra Feeder illustrates how the same design principles can address routine laboratory operations. Together, these tools demonstrate that open, 3D-printed platforms can reduce cost, improve reproducibility, and increase experimental flexibility in zebrafish research, enabling researchers to adapt their tools as scientific questions evolve rather than adapting their questions to available equipment.","abstract_html":"Access to experimental infrastructure remains a major limiting factor in biological research, particularly in behavioral neuroscience and genetic engineering, where many widely used tools are proprietary, expensive, and closed by design. This thesis demonstrates that recent advances in desktop 3D printing and free and open-source software have reached a level of maturity that allows many proprietary research tools to be replaced with open, low-cost alternatives that meet the functional requirements of commercial systems while remaining modifiable, transparent, and affordable. The work presents the OpenZebra toolset, a collection of open hardware and software platforms designed to support zebrafish larvae research. The Agarose Stamping Device provides reproducible larval immobilization with high positional repeatability, replacing fragile manual techniques with a standardized process that can be fabricated, modified, and shared without specialized manufacturing infrastructure. The Zebrafish Larva Interface extends this foundation by integrating 3D-printed mechanical components, commodity imaging hardware, and open-source software to enable quantitative optokinetic response measurements and closed-loop interaction between larval behavior and external systems. Application to pharmacological perturbation studies demonstrates the platform's sensitivity and adaptability, while the OpenZebra Feeder illustrates how the same design principles can address routine laboratory operations. Together, these tools demonstrate that open, 3D-printed platforms can reduce cost, improve reproducibility, and increase experimental flexibility in zebrafish research, enabling researchers to adapt their tools as scientific questions evolve rather than adapting their questions to available equipment.","abstract_has_math":false,"creators":["John Jutoy (22382386)"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2026,"date_issued":"2026-05-01T00:00:00Z","date_published":"2026-05-01T00:00:00Z","updated_at":"2026-07-27T21:33:38Z","subjects":["Engineering, Mechanical","Engineering, Biomedical","Psychology, Behavioral","Biology, Neuroscience"],"languages":[],"rights":["In Copyright"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://doi.org/10.25417/uic.32993807.v1","outbound_label":"DOI","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["John Jutoy (22382386)"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2026-05-01T00:00:00Z"]},{"key":"dc:relation","label":"Dc Relation","values":["https://figshare.com/articles/thesis/Modular_Open-Source_Instrumentation_for_Zebrafish_Larvae_Research/32993807"]},{"key":"dc:type","label":"Dc Type","values":["Text","Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Engineering, Mechanical","Engineering, Biomedical","Psychology, Behavioral","Biology, Neuroscience"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["In Copyright"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["10.25417/uic.32993807.v1"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Access to experimental infrastructure remains a major limiting factor in biological research, particularly in behavioral neuroscience and genetic engineering, where many widely used tools are proprietary, expensive, and closed by design. This thesis demonstrates that recent advances in desktop 3D printing and free and open-source software have reached a level of maturity that allows many proprietary research tools to be replaced with open, low-cost alternatives that meet the functional requirements of commercial systems while remaining modifiable, transparent, and affordable. The work presents the OpenZebra toolset, a collection of open hardware and software platforms designed to support zebrafish larvae research. The Agarose Stamping Device provides reproducible larval immobilization with high positional repeatability, replacing fragile manual techniques with a standardized process that can be fabricated, modified, and shared without specialized manufacturing infrastructure. The Zebrafish Larva Interface extends this foundation by integrating 3D-printed mechanical components, commodity imaging hardware, and open-source software to enable quantitative optokinetic response measurements and closed-loop interaction between larval behavior and external systems. Application to pharmacological perturbation studies demonstrates the platform's sensitivity and adaptability, while the OpenZebra Feeder illustrates how the same design principles can address routine laboratory operations. Together, these tools demonstrate that open, 3D-printed platforms can reduce cost, improve reproducibility, and increase experimental flexibility in zebrafish research, enabling researchers to adapt their tools as scientific questions evolve rather than adapting their questions to available equipment."]},{"key":"dc:title","label":"Title","values":["Modular, Open-Source Instrumentation for Zebrafish Larvae Research"]}]}],"canonical_facts":{"dc:creator":["John Jutoy (22382386)"],"dc:date":["2026-05-01T00:00:00Z"],"dc:description":["Access to experimental infrastructure remains a major limiting factor in biological research, particularly in behavioral neuroscience and genetic engineering, where many widely used tools are proprietary, expensive, and closed by design. This thesis demonstrates that recent advances in desktop 3D printing and free and open-source software have reached a level of maturity that allows many proprietary research tools to be replaced with open, low-cost alternatives that meet the functional requirements of commercial systems while remaining modifiable, transparent, and affordable. The work presents the OpenZebra toolset, a collection of open hardware and software platforms designed to support zebrafish larvae research. The Agarose Stamping Device provides reproducible larval immobilization with high positional repeatability, replacing fragile manual techniques with a standardized process that can be fabricated, modified, and shared without specialized manufacturing infrastructure. The Zebrafish Larva Interface extends this foundation by integrating 3D-printed mechanical components, commodity imaging hardware, and open-source software to enable quantitative optokinetic response measurements and closed-loop interaction between larval behavior and external systems. Application to pharmacological perturbation studies demonstrates the platform's sensitivity and adaptability, while the OpenZebra Feeder illustrates how the same design principles can address routine laboratory operations. Together, these tools demonstrate that open, 3D-printed platforms can reduce cost, improve reproducibility, and increase experimental flexibility in zebrafish research, enabling researchers to adapt their tools as scientific questions evolve rather than adapting their questions to available equipment."],"dc:identifier":["10.25417/uic.32993807.v1"],"dc:relation":["https://figshare.com/articles/thesis/Modular_Open-Source_Instrumentation_for_Zebrafish_Larvae_Research/32993807"],"dc:rights":["In Copyright"],"dc:subject":["Engineering, Mechanical","Engineering, Biomedical","Psychology, Behavioral","Biology, Neuroscience"],"dc:title":["Modular, Open-Source Instrumentation for Zebrafish Larvae Research"],"dc:type":["Text","Thesis"]},"updated_at":"2026-07-27T21:33:38Z"}