Circadian Analysis

 

The marine bristleworm Platynereis dumerilii posesses 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 behaviour of these worms with an automated system. Working together with the Tessmar-Raible and Raible labs, we designed and built a light-tight behavioural 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 behavioural chambers at 15 frames per second, for 7 days continuously.

The project had many technical challenges due to the long duration of the behavioural experiments, and the desire to maximise throughput by recording multiple worms simultaenously. 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 andRaible labs, we developed an efficient image processing solution to extract behavioural activity from the recorded videos. The provided pipeline:

  • Extracted movement data from 25 worms simulteanously, 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 behavioural activity from 25 worms over 7 days (credit: Vinoth Babu Veedin Rajan)
  • Sample frame from analysis (credit: Birgit Pöhn)
  • Images of the constructed assay