loopbio

Video Recording of Multiple Fish Assays

Equipping a whole lab with Motif recording systems

The research in the Couzin laboratory focuses on revealing the principles that underlie collective animal behavior. Fish are a popular model species for studying these principles through analysis of videos of them schooling and swimming together.

We worked with Prof. Dr. Iain Couzin (Max Planck Institute for Ornithology, Department of Collective Behaviour, University Konstanz), to provide a solution for high resolution and high frame rate video recording. Prof. Couzin stressed that the use of higher resolutions and frame rates, over increased scale, would allow the addressing of previously impossible to answer questions in the field of collective behavior.

Besides the technical specifications, it was important to have a system that could grow with the lab as new members joined, and one that was set up with a view toward the future; anticipating the storage and processing demands of a lab with a focus on quantitative understanding of behavior.

Our Motif video recording system was a perfect fit for this project:

High resolution and high frame rate industrial cameras
Capable of 24/7 operation
Lossless and 'lossy' compression
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

Integration with Lab Infrastructure

With an expectation of multiple systems running simultaneously, data management and integration with storage infrastructure was an integral part of this project. We worked closely with the IT staff of the lab and University to design a network architecture for storage and processing of video data. The Motif systems were configured to copy data to a central and backed up storage location after each experiment - allowing the students to access their recordings and process their data from their PCs at their convenience.

Remote Recording and Monitoring of Experiments

When experiments ran in environmentally controlled rooms, it was important that experiments could be started, stopped and monitored without disturbing the behaviour of the animals. Motif's unique web-based user interface was perfectly suited for this task. Within the secure network of the laboratory, students could control experiments remotely from the convenience of the offices.

Starting recording.

Adjusting exposure.

Uploading to storage.

Single-Camera Assays

Based upon the versatility of the Motif system, we consulted on the development of a diverse range of behavioral assays in the Lab. These included:

Numerous single-camera recording systems of several arenas of ~1.20m
Single-camera recording of sub-millimeter organisms in a fume hood
Several multi-camera per PC arena recording systems (for lower frame rates, Motif supports multiple unsynchronized cameras per PC, for an economic recording solution)

A single camera recording from one arena.

Multiple arenas. one computer running motif controls the recording from several cameras.

Multiple-Camera Array

The task was to record an arena of 3m x 3m with at least 1px/mm at 90fps. We recommended 4 cameras with individual camera resolutions of 2048px x 2048px. Such a configuration allowed greater resolution (and frame rate in particular) at lower cost than a single camera. The limited room height restricted the maximum distance between the arena and the camera to ~200cm. To accommodate a wide field-of-view at such a distance with a single camera it would require an exceptionally wide angle lens, leading to perspective distortion in the peripheral regions and reflection from the water due to the now acute viewing angle.

A schematic of the proposed 4 camera design.

We assembled two Motif instances (two-cameras per PC), in a synchronized configuration, such that from a single user interface, the user could record synchronized video from the 4 cameras simultaneously. The finished system allowed recording experiments 24/7 with realtime compression and a resolution of 4000px x 4000px at 90fps.

Cameras securely mounted in the ceiling. The two PCs running motif can be seen in the background. 13 cameras are visible (4-cameras from the system described here, and 9 cameras of a second array).

To combine the images from multiple cameras into a single video, we developed stitchup, an open-source tool for creating video mosaics. After a calibration procedure, stitchup loads the imgstore format synchronized videos from Motif and generates a single video.

The individual camera videos are joined together to make a larger video as though from one camera.

Sample Images

Following the stitching procedure, the videos can be processed by conventional tracking software.