Animal Location Tracker (A3038)

Contents

Description

[20-NOV-24] The Animal Location Tracker (ALT) is a combined motion sensor and telemetry receiver. It will detect signals from any of our telemetry sensors and stimulators, such as our Subcutaneous Transmitter (SCT), Head-Mounting Transmitter (HMT), Implantable Stimulator-Transponder (IST), and Implantable Inertial Sensor (IIS). The ALT is an example of a coil array receiver, as presented in our Telemetry Manual. It provides an array of antennas that decode telemetry messages and measure the radio-frequency power of the signal arriving at the antennas. The power measurements allow the tracker to obtain a power centroid location for each individual implanted transmitters. Because each transmitter has its own unique channel number, we have no difficulty distinguishing between the animals in the cage. The power centroid allows us to measure the activity, movement direction, and proximity of animals cohabiting in a cage.

Figure: Animal Location Tracker (A3038C). A 48 cm × 24 cm array of antennas provides telemetry reception and activity measurement. Two mouse toys and ruler show scale. White lights on left edge show channel reception. Disable lights with the HIDE button.

If we combine the ALT with synchronous video, such as recorded by our Animal Cage Cameras (AACs), the ALT allows us to identify animals seen in the video by correlating their movements with the movements of their implanted transmitters.

Figure: Animal Location Tracker (A3038A) Geometry. Board dimensions and coil locations are the same for the A3038B/C/D, but the coils mounted directly on the base board instead of upon the detector modules.

The A3038A/B/C provides an array of fifteen antennas on a 12-cm grid. The platform is 26 cm × 50 cm and is designed to provide reliable measurement of movement in a cage measuring 22 cm × 46 cm at the base. The ALT receives power and communication through a single Power over Ethernet (PoE) socket at the right side of the platform. To obtain reliable reception and movement measurement, the ALT must operate within a Faraday enclosure, such as our bench-top, stackable FE3B, or our canopy enclosure FE5A. We connect the ALT to an RJ-45 feedthrough in the wall of the enclosure with a shielded CAT-5 cable, and from there to a PoE switch with either a shielded or unshielded CAT-5 cable. We connect our data acquisition computer to the same PoE switch and so record signal and centroid data from the ALT to disk with our LWDAQ Software.

Figure: Detector Module (A3038DM-D). The detector module itself is an Mini PCI Express card that mounts on the ALT base board. The coaxial cable runs to a helical antenna mounted directly on the base board. For a view with the shield covers removed, see here

Our implanted transmitters emit 7-μs bursts of electromagnetic radiation in the range 902-928 MHz. Each burst contains a digital message. Each antenna provides a measurement of radio-frequency power in this same frequency range. When one of the antennas reports that a message transmission is in progress, all fifteen antennas record the power they are receiving. The A3038 saves the transmitted message, along with fifteen eight-bit power values, in its memory, available for download by the Receiver Instrument in the LWDAQ Software, or download and storage to disk by the Neuroplayer Tool. The Neuroplayer contains a Tracker button that opens the Neurotracker Panel, which displays the power centroid of transmitters on the tracker platform.

Figure: Neurotracker Panel Provided by the Neuroplayer. Default parameters to control the location calculation are shown along the top.

If we have several ALTs in the same Faraday enclosure, they will receive signals from transmitters on one another's platforms, so the ALT allows us to specify which channels we want it to record. We can specify a list of channels in the Neurorecorder. By default, the ALT records all channels. The activity lamps on the ALT are bright. Once we are satisfied that our recording is proceeding well, we turn off the lights with the HIDE button, so as to avoid disturbing our subject animals. We turn the lights on again with the HIDE button also.

Versions

[05-APR-23] The following versions of the Animal Location Tracker (A3038) exist.

The A3038D, shown below, is an A3038C modified for operation in environments with high-power radio-frequency interference outside the 902-928 MHz operating band of our telemetry system. If we have a 1-kW, 1840-MHz mobile phone base station on the roof of our animal laboratory, telemetry reception by an unmodified A3038C will unreliable, even within one of our FE3A Faraday enclosures. Our solution is to equip each detector module on the A3038C with an additional coaxial filter that provides further rejection of out-of-band interference.

Figure: Animal Location Tracker (A3038D). Coaxial filters between each antenna coil and its detector module reject interference outside the 902-928 MHz operating range of our telemetry system. Click for high-resolution.

Set-Up

[23-JUN-21] The front end of the ALT is the one with the twenty indicator lamps. The back end is the one with the Ethernet socket. We place the A3038 in a Faraday enclosures with the front end facing us. We plug a shielded network cable into the ALT's Ethernet socket, and we plug the other end of this cable into an Ethernet feedthrough in the wall of our Faraday enclosure. This interior cable must be shielded to stop Ethernet signals interfering with our subcutaneous transmitter signals. If we are working in bench-top enclosure such as the FE3A, we use an Ethernet feedthrough in the back wall of the enclosure. If we are working in a canopy enclosure such as the FE5A), we use an Eight-Way Ethernet Feedthrough (A3039D) taped to the enclosure floor. Outside the enclosure, we the Ethernet feedthrough to a Power over Ethernet (PoE) switch such as the PoE-16, PoE-8, or PoE-5. For this exterior connection we can use either a shielded or unshielded cable. We prefer to use an unshielded cable outside the Faraday enclosure because unshielded cables are more flexible and they also reduce the chance of ground loops in our electrical system.

Figure: ALT System with Four Faraday Enclosures (FE3A). A data acquisition computer (1) runs the Neurotracker software and records telemetry and power centroid positions to disk. A power over Ethernet switch (2) provides communication between eight ALTs and the computer, as well as providing power to the ALTs. Unshielded Ethernet cables (4) connect the switch to a feedthrough (8) in the back wall of each Faraday enclosure (5). A shielded Ethernet cable (3) completes the connection to the ALT (6) inside the enclosure. Each ALT will provide tracking for half a dozen animals with implanted SCTs (7).

When we complete the connection of the ALT to the PoE switch, the ALT should turn on within a few seconds. The white lamps flash all at once, and then the green lamps turn on and stay on to indicate the presense of 3.3V and 5.0V power. The red button on the front end is the hardware reset button. Press and release the red button and the white lamps will flash again. There are two more buttons on the front end, labelled Show and Hide. Press Show and all the indicator lamps on the ALT will turn on, to confirm that they are working. Press Hide once and all the lamps will turn off, with the exception of the two green power lamps, which will remain on. Press Hide again and the indicator lamps are enabled once more.

We connect our data acquisition computer to the same PoE switch. In the LWDAQ Software we open the Neurorecorder in the Spawn menu. We select A3038A and enter the IP address of our ALT. We ship the ALTs with IP address 10.0.0.x, where "x" is the last three digits of the serial number on the ALT circuit board if less than 255, or the last two digits if greater than 254. Thus P0136 ships with address 10.0.0.136, but C0591 ships with address 10.0.0.91. With the Recorder's PickDir button, choose a directory in which to record the ALT signals. Press Reset. We should see the ALT's white lamps flash. We press Record and the Recorder will begin downloading telemetry signals and antenna powers from the ALT and writing them to an NDF file on disk. We should see the amber Upload light shining to show that the ALT is uploading data to our computer, and the Empty light should flash also, to show that our computer is emptying the ALT's data buffer.

Until we place some transmitters on the ALT platform, we will be recording only clock messages to disk. So we now place some transmitters, or animals with transmitters implanted, on the ALT platform. There are fourteen white lamps to show activity from SCT channels. An SCT with channel number n will illuminate lamp number n modulo 16. So channel 12 illuminates lamp 12, and so does channel 28. There is one blue lamp to indicate metadata channel activity. With the Faraday enclosure sealed, we should see the white activity lamps shining steadily for each of our transmitters.

We open the Neuroplayer in the LWDAQ Spawn manu and select our NDF file for playback. We press Play. If we started with no transmitters on the ALT platform, we will see no signals at first, but the Player will soon catch up with the recording and we will see the live data being recorded from the ALT. Press Tracker to open the Neurotracker. The Neurotracker shows us a map of the ALT platform, with the transmitter locations marked in colored dots. We can export SCT signals, ALT power centroid measurements, and ALT antenna power measurements as text or simple binary files using the Player's Exporter. In both the Tracker and Exporter, we specify the ALT location sample rate in samples per second (SPS). The ALT can, in theory, provide one location measurement per SCT sample it receives. So we could set the ALT sample rate equal to the SCT sample rate. But the ALT does a better job of rejecting collisions and interference if we allow at least eight SCT samples per ALT sample. The default ALT sample rate is 16 SPS.

Operation

[15-JUN-23] The A3038 provides an array of antennas. Each antenna is mounted on a detector module. The detector modules are identical. They provide five indicator lamps. The green lamp turns on when the detector module has power and is receiving its clock signal from the base board. The red lamp turns on to indicate an error condition. When the red lamp flashes for half a second, its message buffer has overflowed at least once since the last detector module reset. When the red lamp flashes for one second, its message buffer was empty when the base board controller attempted to read a message from the detector module at least once since the last detector module reset. When the red lamp is on continuously, the detector module's phase-locked loop (PLL) has failed to lock to the base board's 8-MHz clock, which means the detector module's clock is not set to 40 MHz and reception will be impossible. The yellow lamp flashes for 800 μs every time the decoder detects an incomplete incoming message. Whenever one detector module detects an incoming message, auxiliary detector modules measure the incoming microwave power on their antennas. The white lamp flashes for 800 μs whenever a complete message has been received without error. When one detector module receives a message, all detector modules store their power measurements in a buffer. The brightness of the blue lamp increases with the power of received signals. The blue lamp is most useful when only one subcutaneous transmitter (SCT) is moving over the array.

The ALT detector modules are identical circuit boards we plug into sockets on the ALT base board. The detector modules are connected in a daisy chain, where the data from the sixteenth modules moves through all the other modules on its way to the ALT controller. If we unplug the first module in the daisy chain, the controller will be unable to read out any of the remaining fifteen modules. The position of each module in the daisy chain is marked on our A3038C_DMs photograph. If you see red lights flashing, see if you can identify one module that must be blocking the daisy chain readout. If so, follow our ALT_Repair video to remove the ALT cover and re-position the offending detector module.

For each message received from a transmitter, each detector module provides its own eight-bit power measurement. This eight-bit value is a logarithmic measurement of the power received by the detector module from the transmitter when it transmitted the message. The A3038B/C provides an array of fifteen antennas, each connected to a detector module, plus an auxiliary detector module to which we can connect an external Loop Antenna (A3015C) to improve reception or detect background interference. Each message downloaded from the tracker consists of twenty bytes. The first four bytes are the core of the transmitter message, as described in detail elsewhere. The first byte is the channel number. Dual-channel transmitters use two channel numbers to transmit their two signals in separate messages. The second and third bytes are a sixteen-bit sample value. The fourth byte is a time stamp. The ALT messages adds an additional sixteen-byte payload to the core of the message. These sixteen bytes are the sixteen power measurements provided by the detector modules. Their ordering is given by the tracker's geometry drawing. In the case of the A3038B/C, the auxiliary detector power is not shown on the geometry drawing, but it takes the last place in the twenty-byte message.

Our objective is to use the power measurements to obtain a two-dimensional power centroid position that is related to the actual transmitter position in the following ways. The distance moved by the power centroid should be negligible when the distance moved by transmitter is negligible. The distance moved by the power centroid should increase with increasing distance moved by the transmitter. The direction in which the power centroid moves should be strongly correlated with the direction in which the transmitter moves. We the power centroid position is a weighted centroid of the power received from the transmitter in the antenna array, or a weighted centroid of some function of the power. We might use the square root of the power, for example, instead of the power itself.

When we calculate the power centroid position, we start by choosing a sample rate for the calculation. If we choose 8 SPS and our transmitter provides 256 SPS, we expect to have 32 power measurements from each antenna for each of our centroid calculations. We take the median of these, so as to reject corrupted power measurements that arise from transmitter collisions and interference. For each tracker centroid sample, we now have fifteen median eight-bit power measurements, one for each antenna in the array.

The eight-bit power measurements in the ALT message are logarithmic. If the power measurement increases by k, the power has increased by some constant factor g. For the A3038A/B/C, each +33 corresponds to ×10 in power. We could also say that +66 corresponds to ×10 in electric field strength, which is proportional to the square root of the power. We convert the eight-bit power measurements into a value proportional to power with a decade_scale of 33. We convert them into values proportional to the square root of power with a decade_scale of 66. In general, we specify a decade_scale to conver the logarithmic power measurements into a power weight that we will use in our weighted centroid calculation of power centroid. The Neurotracker allows us to set the decade_scale we use for the centroid calculation. We say that power measurement 0 has power weight 1, measurement decade_scale has power weight 10, measurement 2 × decade_scale has power weight 100, and so on.

Once we have the power weights, we multiply each one by the coordinates of its antenna, as given in the geometry diagram, and divide by the sum of the power weights, to obtain the power centroid. We perform the calculation for x and y separately, because they are independent. The result is in the same units as the geometry dimensions. We give ourselves the option of ignoring the power measurements of antennas that are more than extent_radius from the antenna with the maximum power measurement. By default, we se the extent_radius to a value larger than the diagonal of our tracker platform, so we use all antennas. But in the future, if we make a tracker that uses antennas in various places in a maze, the power centroid will be able to tell us where an SCT is in a maze, and the extent_radius would permit us to obtain a robust determination of the animal's progress. We have been using either 33 or 66 for the decade_scale. When we use 66, our power centroid is better-behaved, but contracted towards the center of the platform. When we use 33, our centroid will move to the edges of the platform when the transmitter is above an edge antenna, but the centroid tends to jump at times in a way that does not reflect the actual movement of the transmitter.

Power Consumption

[13-JAN-22] The A3038 draws its power from its Power over Ethernet (PoE) socket, J16, on the right side of the board. An DC-DC converter, L1, produces 5.0 V from the PoE's 48 V. Another converter, U1, produces 3.3 V from 5 V for use by the RCM6700 single-board computer. We measure the power consumption of the A3038 by connecting 5 V directly to the 5-V supply rail, thus by-passing the DC-DC converter, and measuring the current drawing from the 5 V supply. We then assume 80% efficiency in the converter to obtain an estimate of power consumption. By this means, the A3038C consumes 7.8 W.

Design

[15-AUG-24] We construct the A3038 out of a number of electronic sub-assemblies. Each sub-assembly has its own version number, as we present in the table below.

The A3038DM-S is a standalone detector module with five indicator lamp outputs, a coaxial connector for an antenna, a RESET input, an 8-MHz clock input, that runs of 3.3-V power rather than the usual 3.0-V. It plugs into the A3038BB-S, which provides a USB-C connector for power and a BNC connector for the antenna. The two circuits sit in an enclosure with a white RECEIVE indicator visible from all angles.

[12-JUL-24] The Animal Location Tracker (A3038) replaces the Animal Location Tracker (A3032). The A3032 provided an array of antennas to track transmitters, but did not itself decode transmitter signals. The A3038 uses each antenna both as power meter and data receiver. We present the basis of the power centroid measurement in our A3032 Feasibility Study and our A3032 Development. The power centroid provides a robust measurement of activity, direction, and proximity of animals. The correlation between the ALT movement and video blob-tracking permits us to be 100% certain which video blob corresponds to which animal, even when there are several near-identical animals in the field of view.

If you want to control an A3038 with your own data acquisition software, consult the LWDAQ Spectification for details of the TCPIP messages we use to communicate with the A3038. The A3038 acts like a LWDAQ Driver for the purpose of data acquisition. Its controller address space is defined in VHDL as follows.

constant cont_id_addr : integer := 0; -- Hardware Identifier (Read)
constant cont_sr_addr : integer := 1; -- Status Register (Read)
constant cont_djr_addr : integer := 3; -- Device Job Register (Read/Write)
constant cont_hv_addr : integer := 18; -- Hardware Version (Read)
constant cont_fv_addr : integer := 19; -- Firmware Version (Read)
constant cont_crhi_addr : integer := 32; -- Command Register HI (Write)
constant cont_crlo_addr : integer := 33; -- Command Register LO (Write)
constant cont_cfsw_addr : integer := 40; -- Configuration Switch (Read)
constant cont_srst_addr : integer := 41; -- Software Reset (Write)
constant cont_fifo_av_addr : integer := 61; -- Fifo Blocks Available (Read)
constant cont_fifo_rd_addr : integer := 63; -- Fifo Read Portal (Read)

We memory portal address is 63 (0x3F), as in all LWDAQ controllers. But the A3038's memory portal is read-only. The A3038 does not support the stream_write instruction. It does, however, provide a stream_read, and it is the stream read that we use to download telemetry data from the A3038's controller memory. The telemetry data is stored in a first-in, first-out (FIFO) buffer in the controller. To operate an ALT, the data acquisition software begins by writing any value to the Software Reset location (41), which resets the message clock, clears the message buffer, flashes the white lights, and configures the detector modules. After that, keep reading the Blocks Available location (61). Multiply the blocks available by 512 to get the number of bytes available. The maximum value of this counter is 255, so if there are more than 130 kBytes of data available, you will not know it. The ALT data is divided into twenty-byte message. Each message begins with a four-byte SCT record, which we describe elsewhere. After that come sixteen bytes of power measurements. These are the fifteen detector coil power measurements followed by the power measurement of the auxilliary antenna input. When we download from the ALT, we download a whole number of messages, so the number of bytes should be divisible by twenty. We now execute a stream_read and download the number of bytes we expect.

If you want to configure the ALT to record only from certain SCT channel numbers, you can do this by writing commmands into the controller using the Command Register (two bytes) and the Device Job Register. You will find Tcl code for configuring the ALT in Receiver.tcl.

Development

[20-NOV-24] For details of the development and production of the A3038 series circuits, including lists of modifications, see the A3038 Developement page.