Neurologger Synchronizer
Contents
1. Evolocus LLC 177 White Plains Road 42B Tarrytown NY 10591 USA Tel 1 914 329 0035 Fax 1 914 631 3421 E mail info evolocus com Web www evolocus com The following publications were done with the Neurologger 1 Rattenborg N C Voirin B Vyssotski A L Kays R W Spoelstra K Kuemmeth F Heidrich W and Wikelski M 2008 Sleeping outside the box electroencephalographic measures of sleep in sloths inhabiting a rainforest Biol Lett 4 4 402 5 2 Vyssotski A L Dell Omo G Dell Ariccia G Abramchuk A N Serkov A N Latanov A V Loizzo A Wolfer D P Lipp H P 2009 EEG responses to visual landmarks in flying pigeons Curr Biol 19 14 1159 66 3 Pang D S Robledo C J Carr D C Gent T C Vyssotski A L Caley A Zecharia A Wisden W Brickley S G and Frank N P 2009 An unexpected role for TASK 3 potassium channels in network oscillations with implications for sleep mechanisms and anesthetic action Proc Natl Acad Sci USA 106 41 17546 51 4 Brankack J Kukushka V I Vyssotski A L and Draguhn A 2010 EEG gamma frequency and sleep wake scoring in mice Comparing two types of supervised classifiers Brain Res 1322 59 712. several animals carrying Neurologgers can be placed together in one experimental chamber In this case synchronizing labels from the Neurologger Synchronizer will be written in all of them 2 Driver installation To use Neurologger Synchronizer with the TTL CMOS trigging signal or audio output no special software is needed The software is needed only if the synchronization 1s performed through the USB port of the device To use the Neurologger Synchronizer with the USB port one has to install first the necessary USB driver The FTDI interface chip is used in the Neurologger Synchronizer Thus it is recommended to download and install the latest version of the driver from the FTDI web site www ftdichip com The drivers for this chip exist for many operation systems but we tested only under Windows For this reason we describe only installation in this operational system Installation in other systems may have small differences If the user needs to work in the environment different from Windows we may address him to the FTDI web site for additional instructions Windows installation is described lower To install the FTDI USB adapter driver one has to run the installer CDM20802_ Setup exe that can be downloaded from http www ftdichip com Drivers D2XX htm Please choose the driver appropriate for your OS The most common driver is good for the following OSs Windows Server 2008 R2 Windows 7 Windows 7 x64 Windows Server 2008 Wind
3. ed 3 2 Connection to the source of audio signal The Neurologger Synchronizer has one audio input socket and one audio output socket Both accommodate a standard 3 5 mm audio jack Input and output are clearly labeled on the device The idea of using input output is the following If we have to present an audio cue to the animal we can use one channel from two stereo outputs for this task We have selected the Right channel for audio cue In accordance with international agreement the Right channel is connected to the middle contact of the 3 5 mm audio jack and the Left channel to its tip Inside Synchronizer signal goes directly from the Right Audio IN to the Left Audio OUT for compatibility with mono equipment The Left channel of the Audio IN at its tip can transmit the synchronization signal that will make flash of the IR transmitting diodes to store this event in the Neurologger Just one pulse of any duration that can go through the audio cascade is sufficient for recognition by the Synchronizer The proper stereo audio file can be generated in Sound Forge or Matlab The synchronizer has a built in amplifier and a signal of usual loudness can be detected When the trigger is detected the LED 6 Signal flashes on the device Both sources USB and Audio IN can be used at the same time but for proper signal separation a small time interval should be present betw
4. een any pair of trigging events The duration of this interval should not be less than the period of sampling of electrophysiological signal For instance if the Neurologger is configured for sampling at frequency 400 Hz the inter stimulus interval should be larger than 2 5 ms Better larger than 5 ms for reliability in the case of short stimuli However if stimuli are long for instance long bursts this time gap should be kept between the end of the previous stimulus and the beginning of the next If the setup is complicated and stimuli from several sources are desirable one may think about coding of a single event by several pulses to discriminate stimuli of different nature in the record 3 3 Connection to TTL CMOS line If desired the synchronizing TTL CMOS output of external equipment should be connected to the Audio IN socket Signal ground should be connected to the audio Ground of 3 5 mm audio jack the closest to the cord contact and the signal itself should be connected to the middle contact of this jack The synchronizing IR pulse will be sent at the rising edge of the TTL CMOS pulse The maximal frequency of synchronizing pulses should not exceed 1900Hz in a burst and the burst duration should not exceed 255 pulses The maximal number of pulses in a burst is usually not a limiting factor as normally the amount of different events to be coded is small usually one or several And they can be coded by small am
5. l session and other similar time points Putting such event labels is possible with the help of IR receiver add on micro board attached to the Neurologger This microboard also contains 3 D accelerometer to store acceleration of the animal head or a place where Neurologger is attached together with the electrophysiological record Such record can help in some cases in interpretation of the data The IR receiver micro board received signal from the IR emitter s attached usually somewhere at the top of the animal experimental cage and directed to the animal location The I R emitters are controlled by the Neurologger Synchronizer unit described in this manual The Neurologger Synchronizer is designed to receive signals from external equipment that can provide a TTL CMOS output or audio output The Neurologger Synchronizer has also USB interface and it can be attached to any computer with the USB port In software the device is visible as a serial port Thus the user can use any custom written software capable to send data to the serial port of the computer to send time labels to the Neurologger Such software can be written in Matlab LabView or common programming languages like C and Delphi Pascal In the simplest case the user can use Windows Terminal or any other Terminal program for making labels In this case each keystroke of the keyboard can be transmitted and stored in the Neurologger and be precisely aligned with the neuronal data If desired
6. ld be specified in the user software that will access this port g Device Manager File Action view Help H Keyboards FI Ta Mice and other pointing devices B he Modems oe E Monitors H E Network a E ea SCSI are RAID controllers Secure Digital hast controllers E Sound video and game controllers System devices 5i 2 Universal Serial Bus controllers Ae Intel R ICH9 Family USB Universal Host Controller 2934 InteR TCHS Family USB Universal Host Controller 2935 Intel Ri ICH9 Family USB Universal Host Controller 2936 a Intel R ICH9 Family USB Universal Host Controller 2937 Intel Ri TCHS Family USB Universal Host Controller 2938 Intel R ICH9 Family USB Universal Host Controller 2939 ee Intel R TCHS Family USB2 Enhanced Host Controller 2934 Inteli Rt TCHS Family USB2 Enhanced Host Controller 293 USE Composite Device gt USB Composite Device USE Root Hub USB Root Hub gt USB Root Hub LSB Root Hub USB Root Hub iS USE Root Hub is USB Root Hub gt USB Ea Converter 44 iS LSB Serial Converter B It is important to note that this is a virtual serial port For this reason parameters such as communication speed and parity are not important for communication Any values can be specified in the user software Windows Terminal for instance Parameters 19200bps 1 start bit 8 data bits and 1 stop bit without parity work fine The hardware flow control should be disabl
7. nace e Seo cree Evolocus Equipment for Biomedical Research Animal Behavior amp Electrophysiology Neurologger Synchronizer User Manual Evolocus LLC August 2010 ph Table of Contents e Od CUO sean t bet Matadneda tems ER Driver INS CAH AION ae E TA Neurologger Synchronizer connections 0 cece cece ee eee eens 3 1 Connection to USB a c222 sciocensatotveissaressered aawahoeseete 3 2 Connection to the source of audio signal 0 00008 3 3 Connection to TTL CMOS line 0 eee ee ees 3 4 Connection of IR emitters 0 cece cece cece eee ees Configuration of the Neurologger 0 ccc cece ccc ce eee e eee es Contact information and list of publications 005 OMANAANNNAN SB VY 1 Introduction Neurologger Synchronizer is designed for synchronization of the Neurologger 2 and Neurologger 2A with the external equipment Neurologgers are stand along systems that are able to record electrophysiological data in their internal memory without any additional external equipment After the end of experiment the gathered data can be downloaded in the computer with the help of special USB adapter for further processing However in many cases it is desirable to have precise time stamps of certain events in the record This can be some time labels of audio video or other type of stimulus time of the beginning and the end of the experimenta
8. ount of pulses In high frequency neuronal mode of the Neurologger 9600 Hz the pulses will be stored in the data at times exactly when they came However when the sampling rate is low 1600 Hz or lower information about the event will be written in the coded form after termination of the burst This usually does not make a problem as bursts are usually short in time and with low sampling rate there is no need to have a very precise synchronization at ms scale in any case 3 4 Connection of IR emitters Two IR emitters are provided with each device and one or better both of them should be used for the signal transmission to the Neurologger The emitters have 3 5 mm mono audio jacks that should be plugged in the sockets labeled IR LED OUTs 2x The half intensity emission angle of the diodes is 17 They should be directed to the area where the investigated animal is The receiver is quite sensitive to detect the reflected signal from the walls or other objects if animal went out from the area of the direct illumination High sensitivity of the receiver and good engineering of the system in general allows work even with strong background IR illumination Such illumination produced by IR illuminating panels of IR video cameras 1s not usually a problem for transmission of the synchronizing signal For instance Neurologger 7 Synchronizer works well in the popular Phenotyper from Noldus Ambient illumination is not a problem in mo
9. ows Server 2008 x64 Windows Vista Windows Vista x64 Windows XP Windows XP x64 Windows 2000 Windows Server 2003 Windows Server 2003 x64 The executable CDM20802_Setup exe will install the driver without any additional user intervention If the installation goes without mistakes no any messages will be displayed 3 Neurologger Synchronizer connections 3 1 Connection to USB When the driver is installed the Neurologger Synchronizer can be physically attached to the computer This should be done only after the FTDI driver installation described in the paragraph Driver installation If the driver is not installed before the Synchronizer may not be recognized properly When the device is attached the first time a set of small pop up windows will inform you that the new hardware is found First you will be informed that the composite USB device DLP 2232PB is found Afterwards you will see the messages that the USB Serial Converter A and USB serial Converter B are found And at the end that USB Serial Port is found You can verify the correctness of the driver installation in the Windows Device Manager Two additional USB devices USB Serial Converter A and USB serial Converter B and the new USB Serial Port COMn should be visible If the port number does not look convenient it can be changed in properties of the serial port Port settings gt Advanced This port number shou
10. rly to communicate with the add on IR accelerometer micro board To do this one should use Downloader exe utility described in the Neurologger User Manual One should select the checkbox Accelerometer IR board present and the checkbox IR stored 21x About Sampling options Channels lv H V 2 V 3 v 4 Samples per second 4n0 Start delay seconds 0 65535 fo V Accelerometer IF board present No acceleration Jv IR stored C Modulus of acceleration stored C 3 D acceleration stored Logger firmware Not determined Set sampling options Get sampling options Downloading Conversions binary file should be lt 4GB Binary gt Text Binary gt Float321E Gauge runs 2 3 times 0 Remove baseline eee Add markers to the Text Float32lE file Save each channel markers in a separate tent binary Me J Delete temporal files at the end of conversion Average fi sequential values to decrease sampling rate range 1 1e6 Afterwards one should not forget to write new configuration in the logger pressing the button Set sampling options After recording session when converting the data into text or floating point binary format don t forget to select the checkbox Add markers to the Text Float32IE file to store synchronization labels in a separate column 5 Contact information and list of publications Please contact Evolocus LLC in order to purchase Neurologger Synchronizer
11. st cases too However most probably the system will not work well under the direct sunlight If IR background illumination is used and if the animal changes its position fast false positive detections can appear in the record In such cases it is recommended to code the event of interest by several pulses and filter this sequence from the record The last is usually done in Matlab If this approach does not work satisfactorily or is the background IR illumination is very strong one can interrupt the background illumination for a short period usually several ms to transmit the synchronizing pulse To do this one should direct the ground negative line of the IR emitting panel though the jack of the Neurologger Synchronizer labeled SW to GND max 30V 13A The central line should go to the negative contact of the LED panel and the peripheral contact should be connected to the ground or negative terminal of the IR emitting panel power source Note some versions of Neurologger Synchronizer do not have this SW to GND socket When the background IR light switching is used there is no need to attach emitting LEDs to IR LED OUTs 2x as the background light itself will be interrupted in a way to transmit the signal This will work only if the IR emitting panel is built from the IR diodes without any additional circuitry smoothing capacitors etc 4 Configuration of the Neurologger The Neurologger should be configured prope
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