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Research ArticleOpen Source Tools and Methods, Novel Tools and Methods

Rodent Arena Tracker (RAT): A Machine Vision Rodent Tracking Camera and Closed Loop Control System

Jonathan Krynitsky, Alex A. Legaria, Julia J. Pai, Marcial Garmendia-Cedillos, Ghadi Salem, Tom Pohida and Alexxai V. Kravitz
eNeuro 13 April 2020, 7 (3) ENEURO.0485-19.2020; https://doi.org/10.1523/ENEURO.0485-19.2020
Jonathan Krynitsky
2Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology (CIT), National Institutes of Health, Bethesda, MD 20814
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Alex A. Legaria
4Department of Neuroscience, Washington University in St. Louis, St. Louis MO 63110
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Julia J. Pai
4Department of Neuroscience, Washington University in St. Louis, St. Louis MO 63110
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  • ORCID record for Julia J. Pai
Marcial Garmendia-Cedillos
2Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology (CIT), National Institutes of Health, Bethesda, MD 20814
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Ghadi Salem
2Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology (CIT), National Institutes of Health, Bethesda, MD 20814
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Tom Pohida
2Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology (CIT), National Institutes of Health, Bethesda, MD 20814
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Alexxai V. Kravitz
1National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
3Departments of Psychiatry, Anesthesiology, and Neuroscience, Washington University in St. Louis, St. Louis, MO 63110
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  • Figure 1.
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    Figure 1.

    Assembly of the RAT. A, Exploded schematic of the major parts for building RAT. B, Photograph of the parts for building rat. a, 3D-printed housing top. b, OpenMV LCD shield. c, Adafruit DS3231 RTC module. d. Push-button. e. BNC connector. f, 3D-printed housing bottom. g, Custom PCB. h, JST 2 pin connector. i, OpenMV M7 camera. j, MicroSD card with RAT code. C, Photograph of assembled RAT circuit board. D, Photograph of the assembled RAT electronics. E, Photograph of assembled RAT in 3D-printed housing.

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    Figure 2.

    Validation of tracking performance. A, Example images of black and white mice tracked by RAT in light or dark conditions. B, Example xy scatter track plot of data exported from RAT. C, Photograph of experimental validation setup recording the same mouse with RAT and a webcam connected to Bonsai. D, x and y positions from both RAT and Bonsai, demonstrating strong correlation in mouse position data between the two systems.

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    Figure 3.

    Experimental use cases for RAT. A, Demonstration of RAT tracking, showing a circadian rhythm in movement levels over 90 h. Lights were off for duration of experiments, gray bars represent the normal night cycle. B, Schematic of mouse nose-poking to obtain pellets from FED3 device. C, Example track plot for 30 min, showing locations of a mouse when he retrieved pellets from FED3. D, Perievent histogram and raster showing speed of mouse around pellet retrieval events. E, Example track plot for optogenetic real-time self-stimulation experiment. Blue squares show location when blue LED turned on to stimulate direct pathway medium spiny neurons in the striatum. F, G, Quantification of average time on each side of the chamber (n = 4 mice).

Tables

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    Table 1

    Bill of materials

    ComponentNumberCost per unitTotal costSource of materials
    OpenMV Cam M71$65.00$65.00Openmv.io
    LCD shield1$20.00$20.00Openmv.io
    Adafruit DS3231 RTC breakout1$13.95$13.95Adafruit.com
    3D-printed enclosure1∼$5∼$5Any printer will work
    Breakout PCB1$2.00$2.00Seeed.io
    JST right-angle connector1$0.95$0.95Karlsson Robotics
    P/N PRT-09749
    Tactile button1$0.49$0.49Karlsson Robotics
    P/N COM-10302
    Long break away male headers2$0.75$0.75Mouser
    P/N 474-PRT-12693
    Right-angle BNC connector1$2.43$2.43Mouser
    P/N 523-31-5431
    Undercut flat head screws
    4–40 thread
    ⅝’’ length
    7$0.06$0.42McMaster-Carr
    P/N 91099A169
    Li-Ion battery (optional)1$9.95$9.95Adafruit
    P/N 1781
    MicroUSB cable
    (optional)
    1$6.97$6.97Cdwg.com

Movies

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  • Movie 1.

    RTPP_example.mp4. Video demonstrating the real-time-place-preference assay.

Extended Data

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  • Extended data 1

    RAT_code.zip. Code to set the clock and run the tracking algorithm on the RAT. Download Extended Data 1, ZIP file.

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Rodent Arena Tracker (RAT): A Machine Vision Rodent Tracking Camera and Closed Loop Control System
Jonathan Krynitsky, Alex A. Legaria, Julia J. Pai, Marcial Garmendia-Cedillos, Ghadi Salem, Tom Pohida, Alexxai V. Kravitz
eNeuro 13 April 2020, 7 (3) ENEURO.0485-19.2020; DOI: 10.1523/ENEURO.0485-19.2020

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Rodent Arena Tracker (RAT): A Machine Vision Rodent Tracking Camera and Closed Loop Control System
Jonathan Krynitsky, Alex A. Legaria, Julia J. Pai, Marcial Garmendia-Cedillos, Ghadi Salem, Tom Pohida, Alexxai V. Kravitz
eNeuro 13 April 2020, 7 (3) ENEURO.0485-19.2020; DOI: 10.1523/ENEURO.0485-19.2020
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Keywords

  • machine vision
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