Electronics for Neuroscience

General Instructions

General Instructions for using Deuteron Loggers

Brief summary of Instructions

This is a brief summary of the basic steps needed to make a basic neural recording. Each of these steps is explained in more detail on the relevant page.

1) Prepare your animal with suitable electrodes connected to a connector that matches that on the logger, and provide suitable support and housing mechanics for the logger and its battery.

2) Ensure all the required software is present on your computer. See Installing the Software for details.

3) Ensure that a charged battery is connected. See ‎here for further details.

4) Connect the STX4 synchronizing transceiver to the host computer. The computer should beep to confirm that the USB device is recognized and that a suitable device driver is present.

5) Ensure a suitably formatted memory card is inserted into the processor card.

6) Switch the logger on, and connect it to the animal. Alternatively, connect it to the animal and then switch on.

7) Start the LoggerCommand3 program. When it starts, a Start Screen appears. Enter your name and press the large “Connect to Logger” button. When you do so, the software will start the transceiver and then search for loggers that are switched on in radio range of the transceiver.

8) Press “Synchronize” and wait for the settings controls to appear

9) Change any settings of the system as required, for example the reference channel, the low-frequency cutoff.

10) Press “Record” to start a recording.

11) During the recording, you can change some of the settings. Changes of settings can be logged both locally and in the remote system

12) Press “Stop” to stop the recording

13) Switch off the logger and remove the memory card.

14) Insert the memory card into the card reader of a computer, and copy the relevant files as required for analysis.

15) Use one of the provided file viewing utilities or your own software to analyze the data

16) To erase the recorded data, DO NOT attempt to use the host computer’s file manger to do so, but press the “erase all files” button in the Basic Controls tab when the memory card is inserted in the logger. Do not attempt to format the logger’s file system, even if prompted to do so.


General care

The electronic boards of the animal-borne system have fine-pitched connectors and sensitive preamplifiers. Ensure that you handle the connectors carefully, and take precautions to prevent electrostatic discharge. Some of the circuit boards have exposed conductors and components, so take care not to cause short circuits by placing them onto metal objects or a metal table. The circuits should generally be housed in a protective housing that gives them mechanical support and protection from mechanical and electrical damage. However, in some cases, especially when working with small animals, it may be required to mount the headstages directly on electrode assemblies. When making connections to Omnetics connectors, always check the alignment carefully lengthways and widthwise, and be sure that it is not inverted or rotated by 180 degrees.


In systems that use flexible cables to connect the headstages, ensure that the cable does not flex when the animal moves. Although the cables are made of the most flexible wire available, it cannot be guaranteed to endure the repetitive movements that animals typically make between their head and their body. Thus wherever possible the processor board should be mounted on the head of the animal, not its back. In cases where the processor must be mounted on the body of an animal, an appropriate cable assembly must be used.


Transceiver Placement, antenna and radio range

The distance between the transceiver and the logger over which the radio link can reliably work can be quite large, and depends on a several factors, as detailed below. In all cases, the range should be good enough for almost any laboratory setup, and in some cases, some users will prefer to reduce the radio signal strength and thus reduce the working range.

In a clear open space, indoor or outdoors, with full size antennas, and no interference, the radio link can operate for approximately:

  • 15 meters in Monitor mode
  • 35 meters in for regular operation and synchronization
  • Unlimited distance while recording, with no periodic synchronization or system tests

When recording, if no synchronization or system tests are being carried out, the system will continue to record neural data even if the radio link is totally broken, and even if the host computer is accidentally shut down.

In typical lab conditions the range will be at least 10 meters in monitor mode, and at least 20 meters for regular operation.

Factors affecting the radio range

Antenna on transceiver: A standard antenna for the transceiver is about 4.5cm long and is suitable for most lab applications. A longer antenna, typically 12-15cm long, can double the range

Antenna on logger. A quarter-wavelength whip antenna is ideal in terms of radio range. The length of such an antenna is 82mm long for systems using the 915MHz band (e.g. USA) and about 85 mm long for systems using the 868MHz band (Europe). Often this will be inconvenient for animal experiments, and shorter antennas can be used with some loss of radio range

Antenna orientation. The ideal situation is that the transceiver’s and logger’s antennas are both vertical. Other orientations will reduce the range, but often this reduction is not too great, depending on the walls of the room used.

Monitor mode. The radio bandwidth used in monitor mode is greater than that used for all other purposes, so the monitor feature works at relatively shorter range. When using monitor mode, other systems in the same radio space that operate at the same frequency may be unable to communicate. Where such a conflict exists, two different frequencies should be used, or the transmission power of each system should be reduced.

Walls and shields

Some neuroscience labs have electromagnetic shielding walls, and some are even full Faraday cages. Clearly such barriers will weaken or block the radio link. Even ordinary walls attenuate the radio signals.

Interfering signals

If other electronic systems are operating on the same frequency in the vicinity, this may reduce the useful range of the system or even block it entirely. Users of the 915MHz band (e.g. North America) can select a particular frequency within the permitted ISM band, if a persistent source if interference is present. In the European 868MHz band, there is much less scope for selecting a legal frequency, since the 868MHz band is much narrower.

If you find that the communication range is too short, and suspect that there is an interfering radio source nearby, you can use the spectrum analysis feature described here (LINK) If you need to tune your system to a different frequency, contact Deuteron Technologies for details of how to do this.


The animal-borne system is powered by a single-cell lithium polymer battery. These are available in a variety of shapes and sizes. A battery should be selected that is of suitable size for the animal and experiment in question. The standard battery size has a rated capacity of 170mAh and weighs about 3.2 grams. This is sufficient for a measurement session of about 2 hours with 64 channels. Smaller or larger batteries can be used with corresponding mass and operating time. If a long recording is to be started, it is important to start with a fully charged battery.

Batteries can be attached and connected to the system in a variety of ways. The standard connection uses a 3-pin mill-max connector on flexible wires. Alternatively, a battery assembly is available that plugs directly into the adapter board. Where Mill-max connectors are used, the battery is connected to the female connector with its positive connection to the center socket, and the negative connection to one of the side pins. The connectors can be mated in either orientation.   Mill-max connectors are used for battery connections because they are often available in neuroscience laboratories, and users can thus supply and connect their own batteries.

A wide variety of different lithium polymer cells can be used, provided that they include internal protection circuits. Li-Po cells optimized for very high current use (often sold for use with model drones) are not recommended, since they are heavier than other cells for any given capacity, and because their current limit is so high that the protection circuit is not effective in practice. For more information about batteries, see here .


Deuteron’s battery chargers usually take their power form a USB socket and are terminated with a 3-pin male Mill-Max connector to match that of the battery. The USB connector may be connected to any USB power supply or to a USB port of a computer. The Mill-Max connector has three pins: the middle pin is positive and the two outer pins are ground. This allows the battery with a three pin female Mill-Max connector wired with the middle pin positive and either outer pin negative to be plugged into the charger without regard for orientation. The logger has a Millmax connector wired like that of the charger, so that the battery can also be plugged into the logger without regard for orientation.

New batteries should be fully charged before use. The LED indicator on the body of the charger indicates the charger’s state as follows:


██ Blue: The charger is connected to a good power source but is not connected to a battery
██ Pink-Red: The battery is being charged
██ Green: The battery is fully charged


The standard charger provides 100mA of initial charge current, thus it charges a 170mAh battery to 90 of full charge in less than 2 hours and a 100mAh battery is charged in about one hour. If batteries of significantly higher capacity are used (e.g. 320mAh) a charger with higher charging current can be supplied.

Memory cards

The system uses readily available Micro-SD memory cards. Such cards exist with a wide variety of capacities and speeds, and not all available cards are suited for use with the logger. In particular, the speed of memory cards is rated in terms of average data read and write speeds, while this device requires cards whose slowest (not average) write time is always sufficiently low. Unfortunately, manufacturers of memory cards do not normally specify slowest write times, so users should ensure that memory cards used have been checked by Deuteron to work well with this system. Furthermore, since the system is operated using a small battery, it is important to use memory cards whose current consumption is sufficiently low.

You should therefore either use the memory card supplied with your logger, or one that Deuteron recommends for use with your logger. For more details about suitable memory cards see here (LINK)

Formatting an SD card for use in the logging system

Normally, Deuteron supplies all the memory cards necessary to run a recording. In some cases, however, the user may wish to purchase additional cards, which must be formatted prior to use.

For instructions on how to prepare memory cards for use with a Deuteron logger see here (LINK)

Neural Input Connector

The connector of your logger must match that of your electrode assembly. Different loggers use different connectors. For details of the connector on your logger, its pin-out and channel mapping, see the specification manual for your specific logger.

Switching on and the Magnetic switch

Most loggers are switched on and off using a magnetic switch. The advantage of this kind of switch is that it allows the system to be fully sealed in any enclosure, without any provision to be made for the switch. The location of the magnetic sensor is provided in the specification manual for your specific logger. Some loggers will switch on immediately when a battery is connected. Others will only turn on by means of the magnetic switch

To switch the logger on or off, swipe a magnet past the location of the sensor. A typical magnet will work at a distance of about 2cm. The magnetic sensor responds to both north and south poles of a magnet, and can be operated from either side of the processor board.

When the logger switches on, it undergoes some self-tests, and as it does so, the multi-colored LED changes color several times. After about 3 seconds, the LED should be red and flashing, indicating that the system is ready for use. If the LED shows a different color, an error has been detected. The following are some of the LED color codes:


Color Indication
Red, not flashing Amplifier module not connected
Blue Memory card not detected
Red, Flashing All tests passed: Ready

Once the logger is on, you can activate the LoggerCommand program to control the logger’s settings and to start and end recordings.

Copying recorded data

After a recording session you will need to copy the recorded data to a computer for analysis. Remove the memory card and insert it into the card reader of your computer.

Always insert the MicroSD card into an adapter to full-size SD with the write protect switch in the protected state. This is where the tab of the switch is near the middle of the long edge of the adapter. It is not recommended to use the microSD card with a card reader that connects directly to the microSD card, since this cannot ensure that no unwanted writes are made to the card.

Copy the files as needed to computer or server but do not use your computer’s card reader to erase the files.

Viewing and analyzing data

For instructions regarding viewing and analyzing recorded data in Matlab, see Data Viewer ToolData File Manual and Matlab programming examples.

Erasing stored data

Do not erase, rename or modify the stored data files on the logger by using the program manager of your PC. Use the host computer only to copy files from the logger to the computer.

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