SCORHE: System for Continuous Observation of Rodents in Home-cage Environment

Project Collaborators (sorted by Institute): 
Radiation Biology Branch, Center for Cancer Research, NCI
Laboratory of Cell Biology, Center for Cancer Research, NCI
Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI
Eating and Addiction Section, Diabetes Endocrinology and Obesity Branch, NIDDK
Section on Instrumentation, NIMH
Project Brief: 

In collaboration with NCI, NIDDK, NIMH, and FDA, SCORHE is designed to meet the demands of NIH IRP researchers and animal care staff to automatically assess laboratory mice ethology in large-scale settings. SCORHE is comprised of custom video-acquisition and analysis tools developed to quantify mice activity and behavior for short and long (multi-day) durations while housed within a typical home-cage. The specialized hardware was designed to be space efficient, compatible with vivarium cage racks, and animal-facility user friendly. The advanced video analytics algorithms output ethology measures such as locomotion profiles and software-interpreted behaviors. SCORHE hardware targets the ‘natural’ home-cage setting in an effort to eliminate concerns, often associated with traditional mouse monitoring methods, such as circadian rhythm disruption, acclimation periods, lack of nighttime measurements, and short monitoring periods. With mice being the predominant mammalian model used in NIH IRP research, SCORHE is the most practical solution for large-scale use of vision systems in animal facilities, affording researchers and animal care staff accurate long-term activity and well-being measures. SCORHE developments will provide the scientific community an open-source platform for consistent and repeatable acquisition of home-cage ethology measures. More than a dozen SCORHE units being fabricated will provide access to this unique technology to additional IRP investigators. 

SCORHE 3D models and prototype units in vivarium rack

SCORHE hardware is designed to deliver large-scale automated video-based monitoring of research mice housed in standard ventilated racks. (a) A 3D-design model addressing investigator and animal facility requirements and procedures.  (b) A SCORHE prototype built in-house. (c) Two SCORHE units installed in a cage rack (second row from bottom).  SCORHE offers seamless integration while maintaining full rack cage capacity.

Screenshots of SCORHE video and classification example

SCORHE software analyzes incoming video streams to produce detailed time-resolved activity measures for full circadian cycles.  (a) A still image from the front-view camera (top) and the rear-view camera (bottom).  (b) The first processing module segments the incoming images to identify mouse pixels and determine the view in which the mouse is visible. (c) An advanced estimation algorithm reconstructs the corrected 3D position of the mouse head/tail from the fisheye distorted image. (d) A classifier is trained to inspect a sequence of frames and automatically detect one of nine pre-defined behaviors. (e) Time-resolved profiles are generated for each of the pre-defined behaviors.  Shown is the ‘walking’ behavior profile for a 24-hour cycle. The gray shading in the plot indicates the dark cycle, highlighting the nocturnal nature of the mouse.

Tech Transfer: 
  • Technology Dissemination: SCORHE highlighted as a ‘New Methods’ article in the ‘NIH Catalyst’, a publication about NIH intramural research

  • Patent application:  Systems and Methods of Video Monitoring for Vivarium Cage Racks

  • Interagency collaboration: Food and Drug Administration (FDA) contributed resources to SPIS to supplement IRP SCORHE project funding

  • SCORHE website:  Provide open-source access to SCORHE algorithm datasets and code, and fosters interest from industry for technology transfer

  • CDA with industry partner

  • Academic collaboration: NDA signed with Dr. Kristin Branson, Howard Hughes Medical Institute (HHMI) Janelia Farms Research Campus