PiE: an open-source pipeline for home cage behavioral analysis
Over the last two decades a growing number of neuroscience labs are conducting behavioral assays in rodents. The equipment used to collect this behavioral data must effectively limit environmental and experimenter disruptions, to avoid confounding behavior data. Proprietary behavior boxes are expens...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-07-01
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| Series: | Frontiers in Neuroscience |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnins.2023.1222644/full |
| _version_ | 1797768683042373632 |
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| author | Jessie Benedict Robert H. Cudmore |
| author_facet | Jessie Benedict Robert H. Cudmore |
| author_sort | Jessie Benedict |
| collection | DOAJ |
| description | Over the last two decades a growing number of neuroscience labs are conducting behavioral assays in rodents. The equipment used to collect this behavioral data must effectively limit environmental and experimenter disruptions, to avoid confounding behavior data. Proprietary behavior boxes are expensive, offer limited compatible sensors, and constrain analysis with closed-source hardware and software. Here, we introduce PiE, an open-source, end-to-end, user-configurable, scalable, and inexpensive behavior assay system. The PiE system includes the custom-built behavior box to hold a home cage, as well as software enabling continuous video recording and individual behavior box environmental control. To limit experimental disruptions, the PiE system allows the control and monitoring of all aspects of a behavioral experiment using a remote web browser, including real-time video feeds. To allow experiments to scale up, the PiE system provides a web interface where any number of boxes can be controlled, and video data easily synchronized to a remote location. For the scoring of behavior video data, the PiE system includes a standalone desktop application that streamlines the blinded manual scoring of large datasets with a focus on quality control and assay flexibility. The PiE system is ideal for all types of behavior assays in which video is recorded. Users are free to use individual components of this setup independently, or to use the entire pipeline from data collection to analysis. Alpha testers have included scientists without prior coding experience. An example pipeline is demonstrated with the PiE system enabling the user to record home cage maternal behavior assays, synchronize the resulting data, conduct blinded scoring, and import the data into R for data visualization and analysis. |
| first_indexed | 2024-03-12T20:57:51Z |
| format | Article |
| id | doaj.art-388fe556ea854ff28987e55675616ec4 |
| institution | Directory Open Access Journal |
| issn | 1662-453X |
| language | English |
| last_indexed | 2024-03-12T20:57:51Z |
| publishDate | 2023-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroscience |
| spelling | doaj.art-388fe556ea854ff28987e55675616ec42023-07-31T13:08:20ZengFrontiers Media S.A.Frontiers in Neuroscience1662-453X2023-07-011710.3389/fnins.2023.12226441222644PiE: an open-source pipeline for home cage behavioral analysisJessie Benedict0Robert H. Cudmore1The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United StatesDepartment of Physiology and Membrane Biology, University of California-Davis School of Medicine, Davis, CA, United StatesOver the last two decades a growing number of neuroscience labs are conducting behavioral assays in rodents. The equipment used to collect this behavioral data must effectively limit environmental and experimenter disruptions, to avoid confounding behavior data. Proprietary behavior boxes are expensive, offer limited compatible sensors, and constrain analysis with closed-source hardware and software. Here, we introduce PiE, an open-source, end-to-end, user-configurable, scalable, and inexpensive behavior assay system. The PiE system includes the custom-built behavior box to hold a home cage, as well as software enabling continuous video recording and individual behavior box environmental control. To limit experimental disruptions, the PiE system allows the control and monitoring of all aspects of a behavioral experiment using a remote web browser, including real-time video feeds. To allow experiments to scale up, the PiE system provides a web interface where any number of boxes can be controlled, and video data easily synchronized to a remote location. For the scoring of behavior video data, the PiE system includes a standalone desktop application that streamlines the blinded manual scoring of large datasets with a focus on quality control and assay flexibility. The PiE system is ideal for all types of behavior assays in which video is recorded. Users are free to use individual components of this setup independently, or to use the entire pipeline from data collection to analysis. Alpha testers have included scientists without prior coding experience. An example pipeline is demonstrated with the PiE system enabling the user to record home cage maternal behavior assays, synchronize the resulting data, conduct blinded scoring, and import the data into R for data visualization and analysis.https://www.frontiersin.org/articles/10.3389/fnins.2023.1222644/fullbehavioiral neuroscienceopen sourceRaspberry – Pivideo analysishome cage activity monitoring |
| spellingShingle | Jessie Benedict Robert H. Cudmore PiE: an open-source pipeline for home cage behavioral analysis Frontiers in Neuroscience behavioiral neuroscience open source Raspberry – Pi video analysis home cage activity monitoring |
| title | PiE: an open-source pipeline for home cage behavioral analysis |
| title_full | PiE: an open-source pipeline for home cage behavioral analysis |
| title_fullStr | PiE: an open-source pipeline for home cage behavioral analysis |
| title_full_unstemmed | PiE: an open-source pipeline for home cage behavioral analysis |
| title_short | PiE: an open-source pipeline for home cage behavioral analysis |
| title_sort | pie an open source pipeline for home cage behavioral analysis |
| topic | behavioiral neuroscience open source Raspberry – Pi video analysis home cage activity monitoring |
| url | https://www.frontiersin.org/articles/10.3389/fnins.2023.1222644/full |
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