Setup Instructions: ALT and ACC in FE3A

Contents

Introduction
Software Installation
Wall Power Connections
Recording System Connections
Network Communication
Recording
Viewing Recordings
Storage Space
Recording Analysis

Introduction

[02-DEC-21] Here we provide instructions for setting up a recording system consisting of four Animal Location Trackers (ALTs) and four Animal Cage Cameras (ACCs) inside two Faraday Enclosures (FE3A). The instructions are easily extended to eight of each, or reduced to two of each. You will connect the ALTs and ACCs to a Power over Ethernet (PoE) switch, along with your data acquisition computer. You will test the ALTs with sample Subcutaneous Transmitters (SCTs) we supply for your convenience. You will use our general-purpose Long-Wire Data Acquisition (LWDAQ) software to communicate with the ALTs and ACCs. The LWDAQ software is the communication platform within which our Neuroarchiver and Videoarchiver programs operate. You will use the Neuroarchiver to record and examine telemetry signals, and the Videoarchiver to record and view videos. The most difficult steps when setting up the recording system are downloading and installing the software, which can be hindered by your computer's security settings, and configuring your computer to use the PoE switch's local area network, which requires navigating your computer's network settings. If we supplied you with your own data acquisition computer, we have already installed the software for you and configured your computer, so you can skip to the Hardware Connections section.

Software Installation

Note: If we supplied you with a "turnkey system", then we send you your own laptop with our software already installed, so you can skip this section. Open the Firefox browser on the laptop and it will take you to this page directly.

Download and install the latest release of the LWDAQ software by following our installation instructions. The installation procedure is slightly different for different operating systems, but the same zip archive serves Windows, Linux, and MacOS. Download and install the Videoarchiver Libraries by following these instructions. You will end up with directories LWDAQ and Videoarchiver next to one another somewhere in your file system. Make sure there are no spaces in the file system path that points to either of these directories. Don't put them, for example, in a folder called "Program Files".

Create two directories called Telemetry and Video on the hard drive where you want to store your telemetry and video recordings respectively. In the Telemetry directory, make one subdirectory for each of your ALTs, naming it after the serial number of the ALT. In the Video directory, do the same for each of your ACCs.

Run LWDAQ. In the Tool menu, select Videoarchiver and follow these instructions to set prepare the Videoarchiver to record from your cameras. Your objective is to save a CamList.txt file that lists your cameras and the directories into which you want their videos saved. When you open the Videoarchiver again, all you have to do is press Live to see a live camera image, or Record_All to start recording from all cameras. As shipped from the factory, the IP address of an ACC is given by the last three digits of its serial number. So P0159 has IP address 10.0.0.159. The IP address of an ALT is given in the same way by it serial number. There is an exception, however, for serial numbers whose last three digits are greater than 254. For such devices, use only the last two digits. So C0594 would have IP address 10.0.0.94.

We have yet to configure your computer to talk to the PoE switch network, but we will do that after we connect the computer, the ALTs and the ACCs to the switch and make sure they are all powered up.

Wall Power Connections

Connect power to the computer and PoE switch. Each comes with its own power adaptor. If you are operating outside the USA, you will need to match the power adaptors to your local wall power sockets. The PoE switch has a standard IEC-320 power plug. Connect it to the wall socket with any disused computer power cord with your local power plug on the end. The computer power adaptor will either provide the same IEC-320 plug, or will come with a power cord terminated with a USA power plug. In the latter case, we will provide you with a plug adaptor that will connect the USA plug to your local socket.

Recording System Connections

The following video shows how we connect the ALTs and ACCs to the PoE switch and install the ALTs and ACCs in a Faraday enclosure.



Video: Watch Us Set Up Two Animal Location Trackers (ALT) and two Animal Cage Cameras (ACC) in a Faraday Enclosure (FE3A). To view in a separate window, click here.

Check that the white reception lights on the ALT turn on and off as you activate and deactivate your sample transmitters. Make sure as you connect your cameras that they flash their lights three times after about thirty seconds. Three flashes means the camera has booted up successfully. Check that there are activity and green power lights on either side of the connections to the PoE switch.

Network Communication

Note: If we supplied you with a your own laptop, we have already configured it to use its wired ethernet interface to talk to the PoE switch network, and its wireless ethernet interface to connect to the internet. You will have to select the local wireless network and enter the password, but other than that, your communication is ready to go.

Configure the data acquisition computer to communicate with subnet 10.0.0.x using its wired ethernet interface, using our network setup instructions. This configuration can be frustrating, because each operating system, and each operating system version, has its own path to success. When you think you have the wired interface set up correctly, test the connection with the Videoarchiver's camera query function (Q button). You should see a configuration log provided by the camera. Test the connection with the Configurator Tool, which you open from the LWDAQ window's Tool menu. You should be able to read out an ALT's MAC address and software version numbers. Now try to get your computer's wireless network to connect to your local wireless internet. You should be able to browse our website for instructions while running your telemetry system.

Recording

Test the cameras by looking at live images. Run LWDAQ and start a Videoarchiver in the Tool menu. Press the Live button next to any camera to see a live image. Expand the image by dragging its corners. You can view live images from all cameras at the same time if you want to, but the response of your computer may slow down. Detailed instructions for setting up the camera and turning on and off its LEDs are in our ACC set-up instructions. When you are satisfied with the images, press Record_All and recording will begin. Check Verbose to see details of the video segment transfers and the camera microprocessor core temperatures.

Start recording from the ALTs one at a time by returning to the little LWDAQ window and selecting Neurorecorder from the Tool menu once for each ALT. Watch the video below to see how this is done, and how to specify the telemetry recording directory for each ALT and specify its IP address before pressing Start. You may also like to specify the SCTs that will be running on each individual ALT so that the ALT will record signals only from the SCTs in the cage above its platform. If you do not specify the SCTs of each ALT, the ALT will record all signals it receives, which will be most of the signals from all SCTs in the same Faraday enclosure.



Video: Introduction to the Neuroarchiver, Showing How to Start Neurorecorders for Each ALT. To view in a separate window, click here.

Unlike the Videoarchiver, the Neurorecorder records only from one device. It is an entirely independent process dedicated to one ALT. By dedicating one process to each ALT, no malfunction with one ALT can affect recording from another. Because the Videoarchiver is a single process recording from multiple cameras, it is possible for one camera to cause problems for the others, although we have made every effort to prevent any interruption of recording by malfunctions. If you have any problem with the Videoarchiver or Neurorecorder freezing or quitting, please let us know immediately so we can duplicate and fix the problem.

Viewing Recordings

Once you have your telemetry system running, leave it running all the time. You can view the telemetry system recordings live by pressing the Receiver button in any of the Neurorecorder windows. A Receiver Instrument panel will open up and you will see the signals as they are downloaded from the ALTs. You can also view and analyze recordings as they are made with the Neuroplayer. Open a Neuroplayer with the Tool menu of the little LWDAQ window. Select the archive you want to view and press Play.

You can view delayed video from one camera at a time with the MRec buttons (Monitor RECording) in the Videoarchiver. Your view of the recordings will be delayed by a few seconds, which is the time it takes for the camera to compress its video segments, followed by transfer to the computer and staging for display. The ACC and Videoarchiver are designed to provide video that is synchronous with telemetry, not to supply live video. You cannot use the Live button during recording.

You can view your telemetry and video recordings synchronously with the Neuroplayer. But you cannot view videos in this way as they are being recorded. On MacOS and Linux, you will see poor response in the playback when trying to view live videos. On Windows, you will receive an error from the operating system telling you that you cannot view a file that is being written to by another process. Navigation through synchronous telemetry and video is reliable only for recordings that are at least ten minutes old. The tutorial video below shows how to view telemetry and video synchronously with the Neuroplayer.



Video: Demonstration of the Neuroplayer, Showing How to Navigate Through Synchronous Video and Telemetry Recordings. To view in a separate window, click here.

The video files are H264-compressed with key frames every second. They are stored in MP4 containers. You can play them directly with a video player. The telemetry files are stored in our simple NDF format. You can play those only with our Neuroarchiver or with certain programs written by our customers. But the Neuroarchiver provides an exporter that will write ALT position measurements and telemetry signals to disk for you. See our Exporting Data instructions for details.

Storage Space

The ACC has two resolutions available: high and low. The default is high-resolution. The high-resolution videos occupy roughly 3 MBytes/min (eight megabytes per minute) on disk, depending upon how much the animals are moving. With four animals over one ALT platform, each implanted with a two-channel transmitter, and each channel providing 512 SPS (samples per second), the ALT generates 5 MBytes/min. Combining these, we have 8 MByte/min or 11 GByte/day. With four ALTs and four ACCs we have 44 GByte/day.

We recommend at least a 1-TByte (one terabyte or one thousand gigabytes) hard drive in your data acquisition computer. If we supply your computer, its hard drive will be 2 TByte or higher. A 2-TByte drive will permit continuous recording for six weeks. But many studies run for eight or even sixteen weeks, so we recommend you set up a scheme for transferring your data off the computer hard drive once a week.

Recording Analysis

The purpose of our telemetry system is to permit automatic event detection in the recording of biometric signals. In most studies, detection is performed after the experiment, but it can also be performed live so as to initiate stimuli in response to events. For details of processing telemetry recordings see the Neuroarchiver Manual. In particular, the Neuroarchiver's Event Classifier is a well-established system for identifying a variety of events in large sets of data.

The purpose of the ALT's array of detector coils, apart from receiving telemetry signals, is to provide a measurement of the activity of animals over array. We use the Export Panel of the Neuroarchiver to export location measurements, and from these we calculate the distance moved by animals, and so compare their activity. At the time of writing, analysis of the ALT data is in its early stages of development. The activity measurement is robust and simple to implement, but we are working on more sophisticated uses of the measurements, such as comparing the proximity of pairs of animals, and distinguishing between ambulation and shaking.

The primary purpose of the videos is to confirm events detected in the telemetry recordings, such as epileptic seizures, and to permit confirmation of behavioral measurements provided by the ALT. If we feel the need to do so, we can apply video blob tracking to the videos and use the ALT measurements to determine which blob is which in the video. The correlation between ALT movement and blob movement is sufficient to make this determination. We have prototype blob-tracking software available here.

In your efforts to analyse telemetry, tracking, and video, we will provide you with detailed support, including writing code to produce the data in the format you desire, and tailoring event-detection algorithms for your study. When we modify the LWDAQ software for you, you can download the latest version from our GitHub repository. Download the LWDAQ master as a zip archive and replace thew contents of your old LWDAQ directory with the contents of the archive.