Circadian Analysis

Integrated Motif video recording and custom tracking software

The marine bristleworm Platynereis dumerilii possesses both a circadian and a circalunar clock, making it an attractive species to study the molecular basis of biological rhythms in a controlled laboratory environment.

We worked with Prof. Dr. Kristin Tessmar-Raible to replace the manual assay previously used to quantify the behavior of these worms with an automated system. Working together with the Tessmar-Raible and Raible labs, we designed and built a light-tight behavioral chamber and integrated the assay with our video recording system. In order to capture changes in circadian and circalunar rhythms, and to increase throughput, the system uses a high resolution (2046x2026px) camera, recording 25 behavioral chambers at 15 frames per second, for 7 days continuously.

The project had many technical challenges due to the long duration of the behavioral experiments, and the desire to maximize throughput by recording multiple worms simultaneously. No existing commercial product was able to deal with the amount of video data (150Gb per 7 days). The unique features of our motif video recording system made it the perfect match for this project:

  • Extreme reliability - no risk of data loss when recording for days to weeks
  • Ability to save experiment metadata and environmental measurements in addition to video
  • Web based user interface allows users to monitor experiment progress remotely
  • Integration with IT infrastructure to ensure movies are backed up and saved to group network storage
  • Excellent image and compression quality reduces storage costs

Image Processing

Due to the size of the recorded data, existing software packages were unable to process the recorded data in realistic time. Working together with the Tessmar-Raible and Raible labs, we developed an efficient image processing solution to extract behavioral activity from the recorded videos. The provided pipeline:

  • Extracted movement data from 25 worms simultaneously, at 6x real time (so a one week recording was processed in less than two days).
  • Generated data in standard CSV format so researchers could study it in their manner of choice (R, Python, Excel, etc).
These photos show the system and sample analysis,
  • Combined behavioral activity from 25 worms over 7 days (credit: Vinoth Babu Veedin Rajan)
  • Sample frame from analysis (credit: Birgit Pöhn)
  • Images of the constructed assay
Sample activity data from tracking software.
Close up of custom well profile.
Tracking and analysis of 25 wells.
Outer and inner views of the light-tight box.