Animal Cage Camera


Overview

The Animal Cage Camera (ACC) operates with our Videoarchiver software to provide video that is synchronous with the data acquisition computer clock to within ±50 ms. The ACC is a Power-over-Ethernet (PoE) device that requires only one ethernet cable connection to a PoE switch for power and communication. We place the ACC in a Faraday enclosure, connect it with a shielded ethernet cable to to an ethernet feedthrough at the wall of the enclosure, and then with an unshielded ethernet cable to a PoE switch. We connect this switch to our data acquisition computer, and so allow the data acquisition computer to download video from the camera.


Figure: Two Animal Cage Cameras, Version A3034C. The A3034C's wide-angle DSL227 lens and IMX219 image sensor provide a full-color, 148-degree diagonal field of view.

The Neuroarchiver software makes sure that telemetry recordings are synchronized to ±50 ms the data acquisition computer clock. Assuming we have both the Videoarchiver and Neuroarchiver running on the same computer, the result is synchronization of telemetry and video to within ±100 ms.


Figure: The A3034C Held By a Mobile Phone Mount. The mount is made by Evanto. Note the hole above the lens, which gives access to the firmware reset switch.

When commercial CCTV camera systems record continuous video, they produce a sequence of files on our data acquisition computer, each of which is supposed to span a specified length of time. When we view these files, we find that the length of time spanned by each file is a few seconds longer or shorter than specified. Each file has a name that gives its time of creation, and the difference in creation time from one file to the next differs by a few seconds from length of the video contained in each file. When we start viewing a new file recorded by a CCTV system, we must wait a few seconds before the picture establishes itself. As a result of these problems, we cannot rely upon synchronization between video produced by such systems and recordings obtained form our subcutaneous transmitter system. In practice the two chronologies disagree by tens of seconds, and in a manner that we cannot predict or correct for. Our Animal Cage Camera (ACC) is designed to solve these synchronization and viewing problems, and provide superb image quality in both light and darkness.


Figure: Animal Cage Camera and Octal Data Receiver Connections.

The ACC provides video that is synchronous with our subcutaneous transmitter recordings to within ±100 ms over any recording duration. The camera streams its video as separate frames at a fixed rate. These are received by the Videoarchiver process on the video recording computer, where they are assembled and compressed into a video that is synchronous with the local computer clock. Given that the EEG recorded by our subcutaneous transmitters is also synchronized to the local computer clock, the result is EEG and video synchronized to the same clock within a twentieth of a second. In the Neuroarchiver Tool, we specify a directory containing the video files, as well as a directory containing the EEG recording files, we can navigate through the EEG recordings and see the synchronous video displayed automatically.

Version Features Image Sensor Lens Video
A3034C Sits on floor, mounts in mobile phone camera stand, or zip-ties to
shelf structure. Provides 12 white and 12 infrared LEDs.
IMX219 DSL227 820 × 616, 20 fps, H264 crf=23 (HR)
410 × 308, 30 fps, H264 crf=15 (LR)
A3034D Sits on floor, mounts in mobile phone camera stand, or zip-ties to
shelf structure. Provides 12 white and 12 infrared LEDs.
IMX219 DSL215 820 × 616, 20 fps, H264 crf=23 (HR)
410 × 308, 30 fps, H264 crf=15 (LR)
Table: Active Versions of the A3034, With Video Properties. We have "fps" for "frames per second" and "crf" for the H264 algorithm's "constant rate factor". The lower the value of crf, the less compression is used, and the higher the quality of the video output.

The image quality we obtain from the ACC is superior to that of low-cost CCTV systems. The ACC lens's depth of field and sharpness of focus, and the superb exposure compensation of its image sensor, provide clear, sharp images of laboratory animals in poorly-lit cages, even when the camera is only ten centimeters from the cage wall or ceiling. By default, we ship the ACC with focal range 40 cm and depth of field 20 cm to infinity. We can adjust the focus for closer or farther viewing by loosening two screws on either side of the lens, rotating the lens, and fastening the screws again.


Figure: DSL227 Images in White (Left) and Infrared (Right) Light.

The ACC provides both white and infrared illumination that we can use to enhance image contrast, take pictures at night, or generate twenty-four hour illumination cycles. In order to view animals at night in infrared light, our lenses must not include an infrared-blocking filter. Without an infrared-blocking (NoIR) filter, the colors we record will be affected by infrared light from any source. The standard ACC does a poor job of recording colors in sunlight, or when its infrared lights mixes with ambient white light. We recommend operating the ACC in white LED or flourescent lighting during the day, and infrared at night.


Figure: Images of Brightly-Colored Object in White LED Light (Left), Infrared LED Light (Center), and White Plus Infrared Light (Right).

One use of video recordings is to track the movements of individual animals. Given that animals tend to remain in one piece as they move around, and rodents tend to remain the same color, we can treat animals as blobs in image analysis, and track them with video blob tracking algorithms. But when we have more than one animal in a cage, and the animals are near-identical in appearance, and keep vanishing underneath obstacles, and grouping together into larger blobs, video blob tracking cannot distinguish between the animals. But if we have subcutaneous transmitters implanted in our animals, we can use an Animal Location Tracker (ALT) to measure the approximate movements of each animal, compare these movements to those of the blobs produced by blob tracking, and so determine which blob corresponds to which transmitter, which results in unique identification of each blob. We call this disambiguation of the blob tracking by the ALT data. This disambiguation is possible only because the ACC videos are so well-synchronized with the subcutaneous transmitter system, and in particular the ALT's recordings of pick-up coil power reception.

Webcams

We sell the ACC for US$1000 each, with no volume discount. If you can tolerate ±10 s synchronization between telemetry and video, we suggest you instead use Telemetry-Compatible Webcams (TCW). The TCW is a power-over-ethernet (PoE) webcam that we buy on the consumer market. We first test them with our telemetry system to make sure they do not disturb signal reception, and we equip them with the correct cables for integration into our recording system. We sell our TCWs for only $200 each. We recommend you do not purchase webcams yourself for use with our telemetry system. The power converters used in PoE cameras, regardless of their cost, can generate so much noise that they interfere with telemetry reception. You may find that you lose telemetry reception whenever you turn on the camera's infrared lights.

Links

Animal Cage Camera (A3034): A high-resolution, power-over-ethernet camera with remote-controlled white and infrared illumination.

Videoarchiver Tool: Manual for the Videoarchiver, a LWDAQ Tool, which records video from multiple ACCs in such a way that it may be played back synchronously with EEG and ALT recordings.

Neuroarchiver Tool: Manual for the Neuroarchiver, a LWDAQ Tool that plays simultaneous video recorded from ACCs, biometric signals recorded from subcutaneous transmitters (SCTs), and activity monitoring recorded by animal location trackers (ALTs).

Videoarchiver Libraries: Archive of libraries for MacOS, Linux, and Windows necessary to run the Videoarchiver in LWDAQ. Download, decompress, and place the Videoarchiver folder in LWDAQ.app/Contents/ to make LWDAQ.app/Contents/Videoarchiver.

Video Blob Tracking (VBT): A description of how we analyze video frames to obtain the coordinates of animal-like objects. This link leads to our GitHub repository, where we keep the developing software files.

Animal Location Tracker (ALT): A platform of radio-frequency pick-up coils that measures the movement of individual subcutaneous transmitters in a cage above.

Test_21AUG20.zip: Fifty-five 20-s videos with accompanying telemetry from two transmitters mounted on mouse toys.

Test_13JUN19.zip: Four 600-s videos with accompanying telemetry from an animal with an Implantable Sensor with Lamp (ISL). We see the light flashing, and unwanted lamp artifact in the recorded EEG signal, which is perfect for checking synchronization of video.

Test_05JUN18.zip: Ten 60-s videos with accompanying telemetry from four transmitters being handled in a Faraday enclosure.

Parts and Prices: A list of devices and their prices in various quantities.