MC_Rack Manual
Information in this document is subject to change without notice. No part of this document may be reproduced or transmitted without the express written permission of Multi Channel Systems MCS GmbH. While every precaution has been taken in the preparation of this document, the publisher and the author assume no responsibility for errors or omissions, or for damages resulting from the use of information contained in this document or from the use of programs and source code that may accompany it.
Table of Contents Introduction About this Manual Terms of Use Limitation of Liability Important Safety Advice 1 1 2 2 2 First Use of MC_Rack Welcome to MC_Rack Installing MC_Rack 3 3 4 Step by Step Tutorial Using the Step by Step Tutorial Monitoring and Recording Activity Starting MC_Rack Defining the Data Source Advanced Configuration Adding a Data Source Channel Tool Monitoring Activity Continuously Recording Data Starting Data Acquisition and Recording Monitoring and Recording Triggered Activity Trig
MC_Rack Manual Recorder Recording Data Generating Data Files Replayer Loading a Data File File Specifications Replaying Data Displaying Data Display Types Setting up a Display Layout Display Settings Peak Detection Customizing a Display Displaying a Background Picture ASCII Export of Waveforms Data Display (for Monitoring Raw Data) Plot Types Trace Plot Overlay Plot Raster Plot Digital Display (for Monitoring TTL Inputs) Displaying Digital Data Numeric Display Trigger Detector Using the Manual Trigger Trig
Table of Contents Parameter + Spike Analyzer Display Plot Types Trace Plot False Color Maps False Color vs.
1 Introduction 1.1 About this Manual This manual comprises all important information about MC_Rack. It is assumed that you have already a basic understanding of technical and software terms, but no special skills are required to read this manual. Start practicing with the Tutorial. We offer you the opportunity of Learning by Doing, which means that you start directly with practicing without much reading beforehand.
MC_Rack Manual 1.2 Terms of Use You are free to use MC_Rack for its intended purpose. You agree that you will not decompile, reverse engineer, or otherwise attempt to discover the source code of the software. 1.3 Limitation of Liability Multi Channel Systems MCS GmbH makes no guarantee as to the accuracy of any and all tests and data generated by the use the MC_Rack software. It is up to the user to use good laboratory practice to establish the validity of his findings.
2 First Use of MC_Rack 2.1 Welcome to MC_Rack Please read the following paragraphs to understand the general idea behind the MC_Rack program before going on with the tutorial or application examples. MC_Rack is a data acquisition and analysis software. Combined with the hardware, for example MC_Card, (USB-) ME-Systems or (USB-) MEA-Systems, it forms a complete data acquisition system for measuring extracellular activities of excitable cells, in vitro and in vivo.
MC_Rack Manual The MC_Rack help is divided into the following main sections: Step by Step Tutorial: The tutorial introduces basic MC_Rack features for directly setting up a basic experiment. MEA (In Vitro) Application Examples (please see separate document): Main MC_Rack features are explained in detail on the basis of typical applications and demo data files.
First Use of MC_Rack Recommended operating system settings The following automatic services of the Windows operating system interfere with the data storage on the hard disk and can lead to severe performance limits in MC_Rack. These routines were designed for use on office computers, but are not very useful for a data acquisition computer. Turn off Windows System Restore. Turn off automatic Windows Update. Windows Indexing Service deselected for all local disks.
3 Step by Step Tutorial 3.1 Using the Step by Step Tutorial In the following tutorial, you will set up virtual racks for different applications from scratch. The goal is that you learn about MC_Rack features by doing. The racks are quite simple to give you an idea of the software's philosophy and how things work. All racks described in the tutorial are also available on the installation volume.
MC_Rack Manual 3.2 Monitoring and Recording Activity 3.2.1 Starting MC_Rack Double-click the MC_Rack icon or select MC_Rack from the Start menu. The program starts. One window opens automatically. This is your virtual rack configuration, which is blank after program start. Therefore, most commands and buttons are unavailable. You can choose from various software features, so-called virtual instruments, and assemble the virtual rack according to your specific application.
Step by Step Tutorial In the Recorder settings, you select the data streams and channels that you want to save to the hard disk. You define the path and the file in which the acquired data will be saved, and you define other parameters like the recording mode (continuous or triggered), and the maximum file size. The Recorder shows you the currently available disk space on the target hard disk.
MC_Rack Manual MEA60-System Select 2 dimensional (MEA) if you are performing extracellular recordings from microelectrode arrays (MEA) with a MEA60-System with 60 electrode channels. The number and layout of channels is pre-configured and cannot be altered. You have three additional analog channels (A1, A2, A3), and an additional 16-bit digital channel available. The standard BNC connectors for the digital channel on the data acquisition computer support only three digital input bits (0, 1, 2).
Step by Step Tutorial MEA120-System Select 2 dimensional ( MEA) if you are performing extracellular recordings from microelectrode arrays (MEA) with a MEA120-System with 120 electrode channels. The number and layout of channels is pre-configured and cannot be altered. The MC_Card supports seven additional analog channels, but the BNC connectors on the data acquisition computer support only 3 additional analog channels (A1, A2, A3). You have an additional 16-bit digital channel available.
MC_Rack Manual ME-Systems Select 1 dimensional if you are using a ME-System (generally used for in vivo or special in vitro applications). ME-Systems are available with different channel numbers. Define the number of channels provided by the data acquisition (MC_Card or USB-ME), and specify how many electrodes (data amplified by the main amplifiers, for example, a MPA and a following filter amplifier) and how many analog inputs (for example, from a temperature controller or a microphone) are present.
Step by Step Tutorial Data Source Configuration Click "Configuration". Configuration is an option that can also be used with MC_Card data acquisition (64 or 128 channels), but is recommended for the USB based data acquisition systems USB-ME64 / USBME/128 / USB-ME256 or MEA2100-System. When selecting the configuration option, it is first necessary to adjust the number of channels available. After that you can select the amplifier(s) and MEA(s) in use from a drop down menu.
MC_Rack Manual In MEA120-System it is possible to configure both amplifiers independent of each other. Additionally it is possible to configure the MEA layouts of MEA A and MEA B individually. Note: Setting up the configuration of the data source is important for having the correct layouts for MEA A and MEA B during the complete experiment.
Step by Step Tutorial USB-ME16-FAI-System The USB-ME16-FAI System does not require a MC_Card, but uses an internal data acquisition. Data can be transferred via USB 2.0 port to any data acquisition computer. Please see USB-ME16FAI Manual for detailed information. Select USB-MEA from the left Data Source drop down list. The USB-MEA device will be specified on the right Data Source drop down menu: USB-ME16 (S/N: 00001). The number in brackets is the serial number of the device.
MC_Rack Manual USB-ME32-FAI-System The USB-ME32-FAI System does not require a MC_Card, but uses an internal data acquisition. Data can be transferred via USB 2.0 port to any computer. Please see USB-ME32-FAI Manual for detailed information. Select USB-MEA from the left Data Source drop down list. The USB-MEA device will be specified on the right Data Source drop down menu: USB-ME32 (S/N: 00001). The number in brackets is the serial number of the device.
Step by Step Tutorial USB-ME64 / USB-ME128 / USB-ME256 Data Acquisition The USB-ME64 / 128 / 256 data acquisition systems are in principle the same devices, except for the total number of channels. USB-ME256 Data Acquisition The USB-ME256 is an external data acquisition device that uses USB 2.0 connection to transfer digitized data to any connected computer. Please see USB-ME256-System manual for detailed information. Select USB-MEA from the left Data Source drop down list.
MC_Rack Manual Click Configuration in Source Layout. Choose 256 as total number of channels from the drop down list under No. of Channels. In USB-ME256-System it is possible to configure four MEA1060 / MEA1060BC amplifiers independent of each other. Click the Amplifier drop down menus on the left side. Additionally it is possible to configure the MEA layouts for up to four MEAs A and B, C and D independent of each other. Click the MEA drop down menus on the right side.
Step by Step Tutorial On the Edit menu, click Advanced Configuration to configure the software according to the USB-ME256 hardware. Please see Advanced Configuration for detailed information. The dialog Advanced Configuration is for optionally defining as many instances of MC_Rack software as necessary. That means, you are able to work with several MC_Rack versions in parallel, for example, when using the USB-ME256 with up to four MEA1060 amplifiers. With setting "Max.
MC_Rack Manual USB-MEA256 Data Acquisition and Filter Amplification The USB-MEA256 is an external data acquisition device with integrated filter amplifier that uses USB 2.0 connection to transfer digitized data to any connected computer. Please see USB-MEA256 Manual for detailed information. Select USB-MEA from the left Data Source drop down list. The USB-MEA device will be specified on the right Data Source drop down menu: USB-MEA256 (S/N: 00007). The number in brackets is the serial number of the device.
Step by Step Tutorial Wireless Recording System The wireless in vivo recording system is the all-in one solution for amplifying, recording, and analyzing in vivo data from eight channels that uses a wireless connection between headstage and receiver and an USB 2.0 connection to transfer digitized data to any connected computer. Please read the Wireless-System manual for detailed information. Select USB MEA from the left Data Source drop down list.
MC_Rack Manual MEA2100-System The MEA2100 recording system is an all-in one solution consisting of headstage and interface board. The MEA2100-System with integrated amplification, data acquisition, online signal processing, and integrated stimulus generator. You can connect one or two headstages to the interface board. The MEA2100-System uses an USB 2.0 connector per headstage to transfer digitized data to any computer. Please read the MEA2100-System manual for detailed information.
Step by Step Tutorial In MEA2100-System it is possible to configure two headstages independent of each other. MC_Rack identifies two connected headstages as completely different devices. They are defined via the character A or B in the serial number in the right "Data Source" drop down menu. It is also possible to run two MC_Rack instances per headstage, for example for recording from the 2x60 channels of the MEA2100-HS2x60 headstage separately. Please read chapter "Advanced Configuration".
MC_Rack Manual 3.2.3 Advanced Configuration Important: This feature can only be used when working with the USB based data acquisition systems USB-ME256 and USB-ME128. If you use a MC_Card or an USB-ME-16/32-FAI, please do not change the default setting of "Max. Number of MC_Rack Instances = 1". On the Edit menu, click Advanced Configuration to select the maximum number of instances of MC_Rack that can run simultaneously. These instances operate independently from each other.
Step by Step Tutorial Operating 256 channels with USB-ME256 device with one instance of MC_Rack Using an USB-ME256 device, it is possible to operate 256 channels with one instance of MC_Rack. 1. Connect an USB-ME256 device to the data acquisition computer. Start MC_Rack software program. 2. Click Edit: Advanced Configuration and keep the default setting: Max. Number of MC_Rack Instances = 1. 3. Click Edit: Data Source Setup and select USB MEA under Data Source. 4.
MC_Rack Manual Operating 256 channels with USB-ME256 device with four instances of MC_Rack Using an USB-ME256 or an USB-ME128 device, it is possible to operate 128 or 256 channels with two or four instances of MC_Rack. Click Advanced Configuration to select the number of instances of MC_Rack that you want to run simultaneously. Please see screen shot above. Example: Operating an USB-ME256 device with four amplifiers and with four instances of MC_Rack. 1.
Step by Step Tutorial 7. Open the third instance of MC_Rack software program. 8. Click Edit: Data Source Setup and select Block 3 (Channel 129...192) from the right drop down menu. Block 3 corresponds with input C of the USB-ME256. 9. Configure the correct amplifier type and electrode layout for input C. 10. Open the fourth instance of MC_Rack software program. 11. Click Edit: Data Source Setup and select Block 4 (Channel 193...256) from the right drop down menu.
MC_Rack Manual Opening an existing Rack File with USB-ME256 and multiple Instances of MC_Rack If you build up (and saved) a complicated rack in the first instance of MC_Rack which you want to reuse in the second instance of MC_Rack, please do the following: 1. Start the second instance of MC_Rack. 2. Click "Open" in File menu. The dialog "Open Rack Files" appears. Select the desired rack file. 3.
Step by Step Tutorial Operating two MEA2100-32-Systems with multiple instances of MC_Rack Using a MEA2100-32-Systems with two MEAs or two headstages with two MEAs, it is possible to operate up to four devices with up to four instances of MC_Rack, running on a single data acquisition computer. Click “Advanced Configuration” to select the number of instances of MC_Rack that you want to run simultaneously. Please see screen shot above.
MC_Rack Manual 5. Start the second instance of MC_Rack. 6. Click "Data Source Setup" in Edit menu. Select the headstage you want to control with the second instance of MC_Rack via serial number, for example MEA2100-32 (S/N:00018-B). Add the desired data source. The data source and its serial number are displayed in the blue header of the dialog of the "Rack" tab (second instance) as well as after the data source icon.
Step by Step Tutorial Availability of Additional Analog Channels in USB-ME256 (and USB-ME128 respectively) Depending on the selected "Source Layout", it is possible that no, or not all additional analog channels are available. To have full access to the analog channels, please use the "Configuration" option of the data source setup. If other data source layouts are selected, limitations apply: Source Layout 1 dimensional: No additional analog channels are available. Source Layout 2 dim.
MC_Rack Manual In the "Layout" tab, select the "Default Map". The additional analog channels A1 to A4 are displayed. It is also possible to use a custom layout (for example 2x2 electrodes). Please see chapter “Monitoring Activity” for more information about designing channel maps.
Step by Step Tutorial 1. Click the electrode array symbol on the toolbar or click Add MC_Card on the Edit menu. The program detects the MC_Card automatically. If you have no MC_Card installed on the computer, the simulation mode is started automatically, and you will be informed by a message. (If you have a MC_Card, but you still get an error message, the driver installation may be invalid. Please contact your local retailer for support.) You see the MC_Card virtual instrument in your virtual rack.
MC_Rack Manual 3. Click the Hardware tab. Here, you can define hardware related parameters. Please note that the amplifier gain is an intrinsic property of the amplifier and cannot be altered, whereas the input voltage range and the sampling rate of the data acquisition card can be adjusted to your needs. On this page, you will also find hardware related information like the MC_Card driver version and the serial number. Please keep this information at hand when contacting the support. 4.
Step by Step Tutorial 3.2.5 Channel Tool The Channel Tool feature in MC_Rack allows the selection of one MEA electrode as reference electrode. The tool works similar to the offset correction and influences the signal to noise ratio. If there are problems with homogenous noise on all electrodes, the user is able to select one electrode without signal as reference.
MC_Rack Manual 3.2.6 Monitoring Activity Continuously Next, you need a Data Display for monitoring the ongoing activity continuously. Click on the toolbar or click Add Data Display on the Edit menu to add a Data Display to your virtual rack. The Data Display displays the channels in the layout of the Channel Map you have created or loaded. Channel maps are saved as *.cmp files. The default channel map at first program startup is the 8x8 grid of standard MEAs (saved as 8x8mea.cmp).
Step by Step Tutorial Defining the display layout Note: You can set up any channel layout that meets your requirements and save it for later use. You can pick preconfigured channel maps for all MEAs available from Multi Channel Systems from the MCS Channel Maps drop down list. 1. In the tree view pane of the virtual rack, select the Display 1 and click the Layout tab. You see the currently used display layout of the Default Map: The standard 8x8 grid.
MC_Rack Manual 4. Click any electrode number that you want to change and select the desired channel number from the Channel list, or type the channel number with the keyboard. 5. If you want to keep the custom layout for later use, click Save and enter a file name. Option: Advanced Hint: For advanced users only! Adjusting a custom MEA layout to a custom data display layout. Click button Advanced.
Step by Step Tutorial Additional windows appear: Channel Offset, X- and Y- Offset and X- and Y-Extend. These commands concern the data display layout only. Example: Setting up a MEA layout 5 x 5 with electrodes in different sizes.
MC_Rack Manual Customized Display 1. Click User Defined Map. 2. Set up a MEA layout with a 5 x 5 grid using Rows and Columns. The MEA layout appears on the right side of the dialog box and in the data display. 3. Click into the empty squares of the electrode grid and select the desired channel numbers from the Channel drop down menu. The data display shows the channels in the selected layout accordingly. 4. The electrode referring to channel No.
Step by Step Tutorial Selecting data streams 1. Click the Data tabbed page. In this page, you select the data streams that you want to monitor in the display. The Electrode Raw Data stream is already preselected. You can select the Analog Raw Data stream if you have connected a data source to an analog data input (A1 A2 and A3 for the MEA-System).
MC_Rack Manual 3.2.7 Recording Data MC_Rack's philosophy is to strictly separate the actions of all virtual instruments in a rack. That means, that you could record to hard disk completely different data streams and channels than you monitor on the screen. This has the advantage that you can store exactly the channels you are interested in, but it also has the slight disadvantage that all virtual instruments have to be set up separately.
Step by Step Tutorial Choosing the file name and path 1. Click the Recorder tab. 2. Browse your folders and select a path. 3. Type a file name into the text box. 4. Confirm by clicking Save. The file extension for the data files is *.mcd. File size limit The file size is not limited by default, but the user can limit it. When the maximum file size specified by the user has been reached, a new file is generated automatically.
MC_Rack Manual Continuous recording versus triggered recording For recording evoked activity, like LTP experiments or retina recordings, it does generally not make much sense to record continuously. It is recommended to record only the signals of interest following a trigger event, for example, a TTL signal from the stimulator, to save disk space. You can then define the Start Time (before the trigger event) and the Window Extent (total cutout length).
Step by Step Tutorial 3.3 Monitoring and Recording Triggered Activity 3.3.1 Triggering MC_Rack on the Stimulus When recording evoked responses, such as in a LTP or PPF experiment, you usually want to synchronize the data displays and the recording to the electrical stimulation. For this purpose, you can feed in TTL pulses to the digital input bits of the digital input channel. In the standard configuration, three BNC sockets are available for applying up to three separate trigger pulses.
MC_Rack Manual From the Channel list, select the Digital Data D1 channel. A button array appears, one button for each digital input bit. With the Bit button, the logical state (generally HIGH) that generates a trigger event is selected. With the Mask buttons, you can select the bits that you want to use; all unused bits are masked. The digital input bit 0 is already preselected. The logical state that generates a trigger event is set to HIGH. This is fine and you do not need to change it.
Step by Step Tutorial 3.3.2 Monitoring Triggered Activity Next, you need a Data Display for monitoring the ongoing activity. Click on the toolbar or click Add Data Display on the Edit menu to add a Data Display in series with the Trigger Detector to the virtual rack.
MC_Rack Manual Adjusting the ranges 1. Switch to the Display 1 window. 2. You can zoom in the signals by choosing the appropriate range of the y-axis from the Y-Axis drop-down list, or by clicking the arrow buttons. 3. You can select the maximum display refresh rate and maximum x-axis range from the X-Axis drop-down list. 4. You can fine-tune the ranges of the y- and x-axis with the sliders. 3.3.
Step by Step Tutorial 1. You can now either select all channels by clicking the check box next to the Electrode Raw Data stream name, or you can pick single channels by clicking the corresponding buttons. For more information, please see "Channel Selection" in the MC_Rack Features section. Only data from the selected channels will be saved to the hard disk. Choosing the file name and path 1. Click the Recorder tab. 2. Browse your folders and select a path. 3. Type a file name into the text box. 4.
MC_Rack Manual Triggering the recording Again, the displayed data is independent from the recorded data. Thus we need to start the recording on the trigger event generated by the Trigger Detector in the same manner as we triggered the display. This option is only available if there is a trigger stream available, that is, a Trigger Detector in the rack. 1. In the tree view pane of the virtual rack, select the Recorder, and click the Window tab. 2. Select the option Start on Trigger.
Step by Step Tutorial 3.4 MEA2100-System 3.4.1 MEA2100-System Specific Functions of the MEA2100-System The following chapter summarizes all functions and settings of MC_Rack which are specific for the MEA2100-System. You will find the identical information in several subchapters of the MC_Rack manual and in the manual of the MEA2100-System. MEA2100-System Configuration The MEA2100-System is a flexible system, which can be used in different configurations.
MC_Rack Manual After opening MC_Rack as many times as necessary, please open the “Data Source Setup” dialog from the “Edit” menu. This dialog can only be opened in one instance at a time, please do the adjustments in one instance after the other. The example below shows the settings for one MEA2100-HS2x60. Select “USB” and MEA2100 (S/N: XXXXX-A) as Data Source. Select “Configuration” in the “Source Layout”. Please select the type of the connected headstage in the "Amp" drop down menu.
Step by Step Tutorial The appropriate “Amplifier Gain” factor of the MEA2100-System will automatically be entered. The “Input Voltage Range of Data Acquisition Board” divided by the gain is the “Signal Voltage Range”, the maximum size of signals you can record before they get clipped. Please adjust the "Input Voltage Range of Data Acquisition Board" according to the expected size of your signals.
MC_Rack Manual The following dialog appears. Select the tab of any of the three stimulation channels (Stimulus 1, 2 or 3). In the "Stimulus" tab page, you can define the stimulation pulse and select how the stimulation is started and stopped. Click “Stimulus 1” tab page, for example. Defining the stimulation pulse In "Output Mode" you can choose whether you want to stimulate in voltage or current mode. To set up the stimulus pulse or pulse train, please use the eight provided up down boxes.
Step by Step Tutorial Warning: Anodic (positive) pulses can lead to a formation of titanium oxide on the MEA electrodes. When using MEA electrodes of TiN material, use only negative voltages pulses or biphasic current pulses applying the negative phase first. Always regard the safe-charge injection limits. Otherwise, electrodes can be irreversibly damaged by electrolysis.
MC_Rack Manual Starting and stopping the stimulation In the "Trigger" drop down menu it is possible to choose different types of triggers to start the stimulation. The LED next to the Start / Stop button indicates the status of stimulation; the LED turns orange when the stimulation is running, the LED turns grey when the stimulation is stopped.
Step by Step Tutorial Selection of stimulation electrodes Click the “Channels” tab to assign the programmed stimulation patterns to individual electrodes, and to activate the blanking circuit BC, and to operate the “List Mode”. To apply the stimulation pattern of a specific stimulation channel (Stim. 1, 2 or 3) to one or more electrodes, select the desired stimulation channel (Stim. 1 to 3) and click the electrodes you want to apply this paradigm to.
MC_Rack Manual Dedicated Stimulation Electrodes The function “Dedicated Stimulation Electrodes” can be used to further avoid stimulation artifacts on the electrodes surrounding the stimulation electrode, which are sometimes not completely removed by the blanking alone. Usually, the stimulation electrode will be connected to the stimulator output only during the stimulation pulse, and afterwards be switched back to the amplifier to be used as recording electrode.
Step by Step Tutorial When the List Mode is activated, the three stimulator units are coupled to a single starting trigger. The starting trigger is set in the tab of the first stimulator unit, Stimulus 1. In Stimulus 2 and 3, the respective functions are disabled. To uncouple the stimulator units again, close the List Mode dialog.
MC_Rack Manual The command “Remove” eliminates the pattern in the list, which is highlighted in blue. With “Up” or “Down” you can move the patterns to arrange them in that sequence you like to apply them. Click “Download” to download the list of stimulation patterns to the internal stimulus generator of the MEA2100 headstage. To start the stimulation patterns in the list mode, please use the “Trigger Start” in “Stimulus 1” tab of this dialog.
Step by Step Tutorial To monitor the digital data stream you can use the “Digital Display” tool. If a MEA2100 device is connected, the input bits will be labeled according to their function in the digital display. If a MEA2100-32 device is connected, the “Real-time feedback” is not available, respectively the real-time feedback specification 1 to 8 are not available. Therefore the input bits are used for the digital inputs, bit 0 to bit 12 to digIn 1 to 13.
MC_Rack Manual Triggering on Stimulation Pulses from Internal STGs It is possible to trigger on stimulation pulses from any of the three internal stimulus generators. The three internal STG units send a trigger signals with each stimulation pulse on bits 4, 5 and 6 of the digital channel, Stimulus 1 on bit 4, Stimulus 2 on bit 5 and Stimulus 3 on bit 6. Please see chapter “Use of the Digital Channel in the MEA2100” for more details.
Step by Step Tutorial Setting up the Real-time Feedback Software The "Real-time Feedback" works the same way as with the other data acquisition systems of Multi Channel Systems. The "Real-time Feedback" tool must be the first instrument under the data source. Click "Edit" menu and add “Real-time Feedback” or click the real-time feedback icon in the toolbar. Please also read the chapter “Real-time Feedback” for details. However, the dialog of the “Feedback Logic” tab is different for MEA2100-Systems.
MC_Rack Manual 3.5 Wireless-System 3.5.1 Wireless System When using a wireless in vivo recording system, the “Hardware” tab is modified. Please see also chapter “Defining a Data Source” and read the Wireless-System manual. The additional option “Wireless” is for hardware and software control of the wireless in vivo recording system. One recording system can operate with up to four headstages simultaneously, but it is only possible to record from one headstage at a time.
Step by Step Tutorial The button “Switch Off” can be used to send the currently selected headstage from “Stand By” mode to “Switched Off” mode, for saving battery energy. From this mode it is not possible to switch the headstage on again via software control. The blue LED mounted on the headstage of the Wireless-System indicates the recording phases. It can be switched into three modes via radio button. Select “Off” if the laboratory animal is disturbed by the light.
4 MC_Rack Features 4.1 About MC_Rack Features This section provides more detailed information on all features of MC_Rack. The topics are in a systematic order. 4.2 Data Acquisition Settings 4.2.1 Data Source Setup From the Edit menu, select Data Source Setup to configure the software according to your MC_Card or USB based data acquisition and amplifier hardware.
MC_Rack Manual If you use MC_Rack together with devices which do not require a MC_Card, but use an internal data acquisition and USB data transfer, the name of the connected device and its serial number will appear in the right Data Source drop down menu, for example, USB-ME16 or USB-ME256. On the left Data Source drop down menu is "USB MEA" displayed instead of MC_Card. Select the desired device as data source.
MC_Rack Features MEA60-System Select 2 dimensional (MEA) if you are using a microelectrode array (MEA) and a MEA60-System with 60 electrode channels, three analog channels, and a digital channel. The number and layout of channels is pre-configured and cannot be altered.
MC_Rack Manual MEA120-System Select 2 dimensional (MEA) if you are using two MEA1060 amplifiers and a MEA120-System with 120 electrode channels, 7 analog channels, and a digital channel. The number and layout of channels is pre-configured and cannot be altered. Only three of the analog channels (A1, A2, A3) are supported by the BNC connectors installed on the data acquisition computer.
MC_Rack Features Linear (custom) Layouts / ME-Systems Select 1 dimensional if you are using any other type of data source, for example, a ME-System or a custom setup. Define the number of channels provided by your hardware, and specify how many electrodes (data amplified by the main amplifiers, for example, a MPA and a following filter amplifier) and how many analog inputs (for example, from a temperature controller or a microphone) are present.
MC_Rack Manual Data Source Configuration Click "Configuration". Configuration is an option that can also be used with MC_Card data acquisition (64 or 128 channels), but is recommended for the USB based data acquisition systems USB-ME64 / USBME/128 / USB-ME256. When selecting the configuration option, it is first necessary to adjust the number of channels available. After that you can select the amplifier(s) and MEA(s) in use from a drop down menu.
MC_Rack Features In MEA120-System it is possible to configure both amplifiers independent of each other. Additionally it is possible to configure the MEA layouts of both MEAs A and B individually. Note: Setting up the configuration of the data source is important for having the correct layouts for MEA A and MEA B during the complete experiment.
MC_Rack Manual USB-ME16-FAI-System The USB-ME16-FAI-System does not require a MC_Card, but uses an internal data acquisition. Data can be transferred via USB 2.0 port to any data acquisition computer. Please see USB-ME16FAI manual for detailed information. Select USB MEA from the left Data Source drop down list. The USB MEA device will be specified on the right Data Source drop down menu: USB-ME16 (S/N: 00001). The number in brackets is the serial number of the device.
MC_Rack Features USB-ME32-FAI-System The USB-ME32-FAI-System does not require a MC_Card, but uses an internal data acquisition. Data can be transferred via USB 2.0 port to any computer. Please see USB-ME32-FAI manual for detailed information. Select USB MEA from the left Data Source drop down list. The USB MEA device will be specified on the right Data Source drop down menu: USB-ME32 (S/N: 00001). The number in brackets is the serial number of the device.
MC_Rack Manual USB-ME64 / USB-ME128 / USB-ME256 Data Acquisition The USB-ME64 / 128 / 256 data acquisition systems are in principle the same devices, except for the total number of channels. USB-ME256 Data Acquisition The USB-ME256 is an external data acquisition device that uses USB 2.0 connection to transfer digitized data to any connected computer. Please see USB-ME64 / 128 / 256 manual for detailed information. Select USB MEA from the left Data Source drop down list.
MC_Rack Features Click Configuration in Source Layout. Choose 256 as total number of channels from the drop down list under "No. of Channels". In USB-ME256-System it is possible to configure four MEA1060 / MEA1060BC amplifiers independent of each other. Click the amplifier drop down menus on the left side. Additionally it is possible to configure the MEA layouts for up to four MEAs A and B, C and D independent of each other. Click the MEA drop down menus on the right side.
MC_Rack Manual On the Edit menu, click Advanced Configuration to configure the software according to the USB-ME256 hardware. Please see Advanced Configuration for detailed information. The dialog Advanced Configuration is for optionally defining as many instances of MC_Rack software as necessary. That means, you are able to work with several MC_Rack versions in parallel, for example, when using the USB-ME256 with up to four MEA1060 amplifiers. With setting "Max.
MC_Rack Features USB-MEA256 Data Acquisition and Filter Amplification The USB-MEA256 is an external data acquisition device with integrated filter amplifier that uses an USB 2.0 connection to transfer digitized data to any connected computer. Please see USBMEA256 manual for detailed information. Select USB MEA from the left Data Source drop down list. The USB MEA device will be specified on the right Data Source drop down menu: USB-MEA256 (S/N: 00007).
MC_Rack Manual Wireless Recording System The wireless in vivo recording system is the all-in one solution for amplifying, recording, and analyzing in vivo data from eight channels that uses a wireless connection between headstage and receiver and an USB 2.0 connection to transfer digitized data to any connected computer. Please read the Wireless-System manual for detailed information. Select USB MEA from the left Data Source drop down list.
MC_Rack Features MEA2100-System The MEA2100 recording system is an all-in one solution consisting of headstage and interface board. The MEA2100-System with integrated amplification, data acquisition, online signal processing, and integrated stimulus generator. You can connect one or two headstages to the interface board. The MEA2100-System uses an USB 2.0 connector per headstage to transfer digitized data to any computer. Please read the MEA2100-System manual for detailed information.
MC_Rack Manual In MEA2100-System it is possible to configure two headstages independent of each other. MC_Rack identifies two connected headstages as completely different devices. They are defined via the character A or B in the serial number in the right "Data Source" drop down menu. It is also possible to run two MC_Rack instances per headstage, for example for recording from the 2x60 channels of the MEA2100-HS2x60 headstage separately. Please read chapter "Advanced Configuration".
MC_Rack Features 4.2.2 Defining Hardware Settings Before you start building a rack, configure first the software according to your hardware and amplifier. The following example is for MC_Card and MEA1060 amplifier. Select the MC_Card from your rack and click the Info tab to see the channel layout information of your current rack. You cannot modify the settings anymore once you have added the MC_Card or the Replayer to your rack.
MC_Rack Manual Amplifier gain Specify the gain of the amplifier used. The gain is an intrinsic option of the device and can not be altered. Make sure to use the gain the device actually has. Otherwise the recorded data will have wrong voltage values. The default amplifier gain of a MEA1060 amplifier is 1200. For MEA2100Systems the amplifier gain is automatically set depending on the hardware. Any value between 1 and 1,000,000,000 is valid.
MC_Rack Features Sampling frequency As a rule of thumb, the sampling rate should equal five times the highest signal frequency for a good digitized representation of the continuous analog signals. You would, for example, use a 5 kHz sampling rate when using a MEA1060 amplifier with a cutoff frequency of 1 kHz. It should be set according to the steepest slope of the expected signal. If the shape or amplitude of the signal is very important for your analysis, an even higher sampling rate might be appropriate.
MC_Rack Manual 4.2.3 Channel Tool The Channel Tool feature in MC_Rack allows the selection of one MEA electrode as reference electrode. The tool works similar to the offset correction and influences the signal to noise ratio. If there are problems with homogenous noise on all electrodes, the user is able to select one electrode without signal as reference. The voltage value of this reference electrode will be mathematically subtracted sample point per sample point from all electrode signals in the stream.
MC_Rack Features 4.2.4 Grouping Multitrode Channels Channels from electrodes with multiple channels (tetrodes or stereotrodes, for example) can be grouped. This feature will help to analyze signals from multitrodes with MC_Rack or with other analysis tools that can import MC_Rack files in the future. Right now, this feature is new and not supported yet. But we recommend to use the grouping anyway to take advantage of improved analysis features that will be made available in the future. 1.
MC_Rack Manual 1. From the Edit menu, select Data Source Setup. Data Source Setup is only available as long as your current virtual rack is empty (that is, only a Recorder, but no MC_Card or Replayer in the virtual rack). 2. Select Simulation from the Data Source list. Select either Sine Waves, Default or File Source. 3. Choose a data source layout and the number of channels. For more information, see "Data Source Setup".
MC_Rack Features Open a binary file in MC_Rack in simulation mode. Data of this file is repeated in a infinite loop.
MC_Rack Manual 4.3 Data Streams and Channels 4.3.1 Data Stream Types A data stream can include several channels of the same data type. The term channel means the data from a single MC_Card input pin, that is, electrode. Several different data streams can be generated, handled, processed, and recorded by MC_Rack.
MC_Rack Features chapter About Digital Data and Binary Code under MC_Rack Features, General Aspects. Trigger: Generated by a virtual Trigger Detector. A trigger is used to control virtual instruments or to record triggered data. For example, you can use signals from an external device (for example, from the Sync Out of a STG) for triggering. For electrode raw data, parameters, or filtered data, you can define a threshold for triggering. You can define a bit pattern for using digital signals as a trigger.
MC_Rack Manual If you want to select or deselect all channels of a stream, check the box next to the stream name in the tree view. Note: Click a data stream first to display the corresponding button array. Make sure you have selected the appropriate stream when selecting a channel. 4.3.3 Continuous and Triggered Data You can create either continuous or triggered data files.
MC_Rack Features When using the Replayer for replaying triggered data, make sure all other virtual instruments in your rack are set up according to the data type. It is not possible to display triggered data streams continuously (as there are "gaps" between the sweeps where no data was recorded). The maximum x-axis range is limited by the sweep length. See the File Info of the Replayer to obtain all necessary information on the data file, such as the sweep length.
MC_Rack Manual 4.3.4 Averaged Data Averaged Data, that is, a data stream generated by an Averager, is a special kind of triggered data. Only the last sweep of each averager cycle is added to this data stream. Therefore, a socalled Avg Trigger is saved together with the Averaged Data stream (not to be confused with the Averager Trigger that triggers the Averager). This Avg Trigger marks these last sweeps of a cycle.
MC_Rack Features Click the Window tabbed page and select the option Start on Trigger. Select the Avg Trigger that was recorded together with the Averaged Data stream. 1. Click the Start button to start the Replayer. The averaged data sweep will appear at the time point when it was generated during the recording (here: after summing up 20 sweeps). Overlay of averaged and raw data.
MC_Rack Manual 4.3.5 Digital Data and Binary Code Only two voltage levels are allowed as an input of the 16 digital channels: 0 Volts or 5 Volts. This means, that each channel can have either the state high (5 Volts), also called 1 or On, or low (0 Volts), also called 0 or Off. For example, if you use the Sync Out of a stimulus generator (STG) or another external device to trigger the recording, you can connect the device to one of the 16 digital channels.
MC_Rack Features 4.4 Recorder 4.4.1 Recording Data In MC_Rack, the rack you use to record and analyze data online and offline, and the data files are principally independent from each other. You can reuse a rack for several experiments and generate separate data files. You can then load the generated data file with another rack later for further offline analysis. The Recorder is used to record data acquired by a data acquisition device or data generated by an offline analysis to your hard disk.
MC_Rack Manual 1. Click the data stream that you are interested in, that is generally the Electrode Raw Data stream. The available electrode channels appear in a button array on the right side. 2. You can now either select all channels by clicking the check box next to the Electrode Raw Data stream name, or you can pick single channels by clicking the corresponding buttons. For more information, please see "Channel Selection" in the MC_Rack Features section.
MC_Rack Features Recording triggered data When you record data that is triggered by an event, for example the response to a stimulation, please make sure that the Recorder is operated on this trigger, too (not continuously, to save disk space. Triggered data needs much less disk space than continuous data. Add a Trigger Detector to your rack and start the Recorder on the trigger event.
MC_Rack Manual It is important to know that MC_Rack never modifies or overwrites any existing data file. That means, in an offline analysis (using the Replayer), the extracted parameter streams are stored in a new data file. Therefore, you need to specify a file name and path in the Recorder for both online and offline analysis.
MC_Rack Features 4.5 Replayer 4.5.1 Loading a Data File Data files can be stored separate from the rack files. Use the Replayer to load a data file into your current rack. You can browse your folders and select an appropriate data file or select a file from the Recent Files list. For replaying a data file, you need a virtual rack with a Replayer as the data source instead of the data acquisition device. Setting up a rack for offline analysis 1. Create a new rack file by clicking New on the File menu. 2.
MC_Rack Manual 4.5.2 File Specifications Some information about the experiment is saved together with the data. This information is displayed on the File Info page. It is very important to adjust other tools in the rack according to this information, especially if you have triggered data. See also "Triggered Data" for more information on this subject. The following additional information is stored.
MC_Rack Features Hint: If you want to graph (already extracted) parameters, such as the spike rate, without a further offline analysis, replay only the parameter streams in the Parameter displays, with no further Data Display or other instrument. The replay speed will be much higher, and you will get the graphs much faster. Each virtual instrument in the rack will decrease the maximum Replayer speed.
MC_Rack Manual 4.6 Displaying Data 4.6.1 Display Types You can flexibly define the electrode grid for all displays. You can define not only the channels to be displayed, but also the position of the channels in the display. For example, you can arrange the electrode channels in the typical MEA layout, but you can also customize the layout freely according to your experimental setup. All data streams that you have assigned to a display are shown on this display.
MC_Rack Features The channels of MEA A are tagged with an "A". Likewise, the channels of MEA B are tagged with a "B". If you have a MEA60-System (or an USB-ME64-System) in use, only channels of MEA A are available. If you have a MEA120-System (or an USB-ME128-System) in use, you can choose between MEA A and B. Channel maps for MEA A and B have been preconfigured, but of course you can set up any custom or "mixed" channel layouts as well.
MC_Rack Manual 4.6.3 Display Settings You can select the range and refresh rate of the display from the drop-down lists. In addition, you can zoom the display by moving the sliders. MC_Rack stores the last two seconds of recorded data streams in a temporary virtual memory. Therefore, it is not possible to set the time scale wider than 2 s. If you run the display in triggered mode, the sweeps start with the trigger event = time point 0.
MC_Rack Features Zoom into a part of the displayed sweep by clicking and dragging the sliders with the mouse. Or select a slider with the mouse (a selected slider is highlighted in white) and move it by pressing the LEFT or RIGHT arrow key. For larger steps, press the PAGE UP / DOWN key. Reverse Display Changes the display background color from white to black. Automatic Zoom Please click on the data display with the left mouse button. The following menu appears.
MC_Rack Manual With Peak Detection, the highest (max) and the lowest (min) value of the five data points are taken and connected by straight vertical line. Peaks are preserved in this way. On the other hand, this feature needs a higher computer performance for the internal data handling. You may want to deselect this option when you have a limited computer performance. The following error message appears when the system is at its limits.
MC_Rack Features 4.6.5 Customizing a Display Showing and hiding the axes bar * You can hide the axes bar on top of the display to save space and obtain a larger view of your data. Right-click anywhere in the window and deselect Display Header. Showing and hiding the data stream names * You can show the data stream type of each channel. Right-click anywhere in the window and select Display Labels. Using the crosshairs * Right-click anywhere in the window and select Display Crosshairs to show crosshairs.
MC_Rack Manual 7. Type in the number of the electrode according to the MEA layout, for example 78. The data traces appear on top of the picture. Hint: If you have made a mistake, simply repeat the assignment from step 5 to 7. 4.6.7 ASCII Export of Waveforms Click in the display header (not in main menu tool bar) to save the displayed data as a tabdelimited ASCII file (text without formatting). The format is tab-delimited ASCII, so that the file can easily be loaded into other applications.
MC_Rack Features 4.7 Data Display (for Monitoring Raw Data) 4.7.1 Plot Types Click to add a Data Display to your rack. You can choose between different plot types, depending on the data stream type. When displaying Raw Data, only the Trace plot is available. Trace plot: The voltage traces are plotted. Overlay: Spike cutouts are overlaid. Raster plot: The detection events of spikes are plotted. Use this plot type to make spike patterns visible, for example in relation to a stimulus. 4.7.
MC_Rack Manual ASCII Export The created file has the following structure. The first column is the x-axis (time). Each following column represents a sweep, in the order of plotting, that is the first column contains the first sweep, and so on. The first row specifies the Spike Sorter tags. Untagged sweeps are specified by Unit = 0. Sweeps can be tagged by units 1 to 3. The second row are the measuring units. The following rows contain the data.
MC_Rack Features Using a raster plot The Raster plot is only available for spike data streams. Make sure you have a Spike Sorter in the rack, or replay a data file containing spike data streams. 1. Add a Data Display to your virtual rack configuration (in serial with the Spike Sorter). 2. Click on the Display in the virtual rack tree pane to select it. 3. Click the Data tabbed page of the Display. Select only the Spikes data stream. 4. Select the Raster Plot option.
MC_Rack Manual 4.8 Digital Display (for Monitoring TTL Inputs) 4.8.1 Displaying Digital Data The Digital Display is used to view either the logical state of the 16 digital channels, or to display the 16-bit encoded decimal number of the binary data (see "Numeric Display"). It is only available if the data source you are currently using produces a Digital Data stream. The Digital Display has features similar to the Parameter Display type.
MC_Rack Features See "About Digital Data and Binary Code" for MC_Rack Features. 1. On your rack, click the Digital Display. 2. Click the Settings tab, and then click Decimal Number. The Digital Display is empty now. If you click Start, the actual decimal value based on the 16-bit binary value of the digital data stream is displayed. 4.9 Trigger Detector 4.9.1 Using the Manual Trigger The function "Manual Trigger" allows the user to generate a trigger event manually from within MC_Rack.
MC_Rack Manual Click Trigger tab. Select “Manual Trigger” from the Channel drop down menu. When MC_Rack is displaying or recording data, the button “Trigger” is active. The number of user defined trigger events will be counted up in the small display “Trigger Count”. Alternatively to the Trigger button in the Trigger dialog, you can also use the manual trigger icon in the main menu toolbar to generate a manual trigger timestamp.
MC_Rack Features To display data and manual trigger, please select the desired data streams in the “Data” tab of the display. The display has to be placed in dependency of the Trigger Detector 1 in the virtual tree. When replaying a Rack file with manual trigger events, the timestamp and its number will appear in one channel of the display.
MC_Rack Manual You can select the digital input channels that will be used by the Trigger Detector. All other channels are masked, that is, are not considered at all. Click a Mask button to select an input channel. For example, in the preceding screen shot, TTL signals are accepted only on the digital channel 0. All other channels are masked. This is very important if you do not have all 16 channels in use, that is, connected.
MC_Rack Features 4.9.4 Triggering on Biological Signals You can define a threshold for triggering on biological (analog) signals from Analog Raw Data, Electrode Raw Data, or Filtered data streams. Select the appropriate data stream and channel from the Channels list. If you select the option Negative Slope, the fall of the curve is regarded. If you select Positive Slope, the rise is considered. The following picture illustrates how the trigger detection works.
MC_Rack Manual 4.9.5 Triggering on Extracted Parameters Similar to the triggering on raw data streams, you can also define a threshold for an extracted parameter stream to generate trigger events. For example, you can trigger the recording only if the spike rate reaches a threshold level. Select the appropriate parameter data stream and channel from the Channels list. If you select the option Negative Slope, the fall of the parameter curve is regarded.
MC_Rack Features Single or periodic trigger event If you use a periodic trigger, you define the start time (Wait), when the trigger occurs the first time, and the time interval, when the trigger will reoccur after an event. You can choose whether the trigger shall occur a fix number of times, or whether it shall occur continuously (option Cont.). Predefined list of trigger events 1. If you want to use predefined trigger times, select the option List. 2. Click Edit List to set up a list of trigger events.
MC_Rack Manual 4.10 Automatic Feedback 4.10.1 Digital Output To use this feature, you need a DigOut connector for your computer and the MC_Card driver version 2.5 or higher or an USB based data acquisition device. You can use the Digital Output instrument to apply a feedback triggered by a signal or a parameter stream. Set up a Trigger Detector first. You can then use the generated trigger to apply a digital pulse via the digital output channels of the MC_Card or an USB based data acquisition device.
MC_Rack Features 4.11 Real-time Feedback 4.11.1 Real-time Feedback Introduction The real-time feedback feature represents a significant improvement in signal detection and processing. Previously, the digitized signals were processed by the computers main processor, which involved the operating system and resulted in unpredictable and rather long delays between the actual event and its’ detection.
MC_Rack Manual Setting up the Hardware To generate real-time feedback stimulation to a biological sample, you need an advanced data acquisition system (MEA2100-System, USB-MEA- / ME-System), and a stimulus generator STG. The digital output channel of the data acquisition has 16 bits. Bit 0 is accessible directly via Lemo connector. In MEA2100-Systems bit 0 to bit 3 are separately available via Lemo connectors, but you do not need a cable connection, because of the internal 3-channel STG.
MC_Rack Features The data trace (blue), the detection level (black), and the generated TTL pulses (red) are displayed in one window. It is possible to toggle the display window in the "Digital Hardware Filter" tab. The real-time feedback has to be the topmost tool in the hierarchical order of MC_Rack program below the data source, because the raw data stream is influenced by the digital hardware filter of the DSP. MC_Rack processes this data stream only, and so do all instruments and the recorder.
MC_Rack Manual When recording with a MEA2100-System, the digital display is labeled: The first four rows display the “DigIn” channels for bit 0 to bit 3. The next three rows show the “Blanking” signal 1 to 3 on bit 4, bit 5, and bit 6. “Zero” is associated with bit 7. The following rows display the “RF” real-time feedback associated to bit 8 to bit 16 on channel 1 to 8. To record the digital stream, created via real-time feedback, please enable the respective check box in the “Channels" tab.
MC_Rack Features Digital Hardware Filter In the "Digital Hardware Filter" tab, it is possible to switch the real-time feedback feature on and off, and to define the characteristics of the digital hardware filter that gets applied to the data before it goes through the signal detection algorithm. Using a filter is not obligatory for real-time feedback. It needs Digital Signal Processor (DSP) resources and time for calculation.
MC_Rack Manual Note: Please use first order filters whenever possible. Higher order filters tend to be unstable and oscillate, especially when using very low or very high cutoff frequencies. Warning: Please keep an eye on the “Performance” window. The window shows the percentage of time available between two samples that is needed for real-time feedback calculations (filtering and feedback logic). It should never exceed 90 %.
MC_Rack Features A time interval of 500 ms is used to calculate the standard deviation. You can set the factor by which the standard deviation is multiplied to set the detection threshold numeric updown box. Click “Refresh” button to calculate the standard deviation from the currently recorded data, and to apply the result. It depends on the distribution of noise and spikes, which factor should be used. The higher the spike rate, the lower the factor can be set.
MC_Rack Manual Select the “Event Duration” in milliseconds from the numeric updown box. The event duration is the time after a crossing of the detection threshold that the detection condition is considered as fulfilled. This duration influences the length of the resulting feedback TTL, and is especially important when the input from several electrodes is combined with the “AND” and “OR” function (see below).
MC_Rack Features Select from the “Spike Count” drop down menu either “Single Spike” or values from 2 to 100. This corresponds with the number of spikes that have to be detected in the defined time window to fulfill the criteria to generate a feedback. The frequency resulting from the selected combination of time window and spike count is also shown in the drop down menu in brackets.
MC_Rack Manual In case of rate detection, the logical state becomes TRUE from the detection point of the last event that is needed to fulfill the rate condition till the end of the event duration. If the rate of detected events stays above the rate threshold, the logical state will remain TRUE as long as the rate condition is fulfilled. In the example below, a window of 200 ms and a rate of five events per window is set as condition.
MC_Rack Features Examples: The following examples further illustrate the possible combinations of the Feedback Logic. In example one, single spikes are detected on two channels combined with the condition OR. Hence, the logical state of each channel is TRUE from the detection of an event till the end of the event duration (shown in red). As the two channels are combined with OR, a TTL is generated as long as any of the two channels, or both, have the logical state TRUE.
MC_Rack Manual 4.12 Filtering Data 4.12.1 Filtering Data The Digital Filter tool can be used online or offline. Displays in dependence of filters can show the unfiltered and filtered data stream at the same time, so it is possible to directly monitor the effect of the filtering on the data. This is especially important because all filters are known to distort signals. Keep in mind that you may need a higher sampling rate to avoid aliasing.
MC_Rack Features Adding a filter to your rack 1. To add a virtual filter to your rack, click "Add Filter" from Edit menu, or click the Filter button on the toolbar. 2. Click the Channels tab and select the channels you like to be filtered. Click the Filter tab to select the filter type. If you choose the Butterworth filter you have to define high or low pass and the cutoff frequency. If you select the Savitzky-Golay filter you have to define the order and the "Number of Points" used for averaging.
MC_Rack Manual Signal distortion Though filters present an easy and convenient way to remove unwanted signals from your data, filters should be used with care. All filters (analog and digital) distort signals, especially if the signal frequencies lie near the cutoff frequency. You should be aware of the fact that the signal amplitude may be modified by a filter, and that the signal may be shifted as well.
MC_Rack Features 4.12.2 Filter Characteristics Bessel A Bessel filter is a type of linear filter with a maximally flat group delay (maximally linear phase response). Analog Bessel filters are characterized by almost constant group delay across the entire passband, thus preserving the wave shape of filtered signals in the passband. Butterworth The Butterworth filter is designed to have a frequency response which is as flat as mathematically possible in the passband.
MC_Rack Manual Bandstop Resonator In signal processing, a bandstop filter is a filter that passes most frequencies unaltered, but attenuates those in a specific range to very low levels. A bandstop filter with a high Q factor has a narrow stopband. Please see the following pictures.
MC_Rack Features Example: This can be demonstrated by the following experiment. A regular 1000 Hz signal (from a pulse generator) is applied to electrode input channels of the MC_Card. In this experiment, this signal represents the high frequency noise that should be removed. A 100 Hz Low Pass filter is used to remove this high frequency "noise" signal. At a sampling rate of 5 kHz, signals up to 2.5 kHz are safe from aliasing, resulting in a good sampling and filtering result.
MC_Rack Manual 4.12.4 Downsampling The MC_Rack downsampling feature offers the possibility to generate raw and filtered data streams with different sampling frequencies. This can help to avoid huge amounts of resulting data when recording more than one data stream. For example, you can record spikes with a high sampling rate, and a second filtered data stream with slow field potentials with a lower sampling rate (please see the example at the end of the section).
MC_Rack Features MC_Rack sets the cutoff frequency of the filter automatically. A second dialog will appear and prompt the user to select a cutoff frequency in the possible range (0.1 to half of the downsampling frequency in Hz). Please type in a number in the denoted range. Note: The second dialog is generated directly by Windows, and will therefore appear in the language set in the operating system.
MC_Rack Manual 4.13 Spike Sorter 4.13.1 Spike Detection Methods The virtual Spike Sorter instrument is used for extracting spikes from the raw data, and for sorting spikes into up to three single units per electrode (channel). There are two ways of detecting and extracting spikes with MC_Rack. One method uses a threshold, the other recognizes the shape, that is, the amplitude and slope of a curve. Both methods regard either the rise or the fall of a curve, depending on your settings.
MC_Rack Features 4.13.2 Detecting Spikes by a Threshold You can define a threshold (spike detection level) for each channel separately. All peaks that cross the threshold are detected. Spike traces are cut out around the detection event. The resulting spike cutouts form a new data stream that can be further processed by other tools, that is, sorted, analyzed, displayed, and so on. See also the preceding illustrations "Spike detection" and "Voltage threshold not reached".
MC_Rack Manual Only waveforms that satisfy both criteria (slope and amplitude) are considered spikes. See also the preceding illustrations "Spike detection" and "Not detected waveforms". 4.13.4 Spike Cutouts You can define the size of the spike cutout in the ranges of 100 ms Pre-Trigger and 1500 ms Post-Trigger times.
MC_Rack Features 4.13.5 Spike Sorting Most often, spikes do not represent a single unit activity, but are derived from multiple neurons. Spikes from separate neurons usually have different shapes and a different rhythm. To interpret an experiment, it is often very important to sort spikes into categories, thus separating single unit spikes. In MC_Rack, you can sort spikes into three groups. The sorted spikes can then be displayed by a Data Display. A special overlay display for spike sorting is provided.
MC_Rack Manual The following illustration shows the activity of two neurons, as spike cutouts on a small time basis. The first (red) signal has one peak, the second (yellow) spike waveform shows a small peak followed by a bigger peak. The window bars are positioned at the time point where both signals differ most. 100 spikes are overlaid in this plot.
MC_Rack Features 4.13.6 Burst Analysis The “Burst Detection” option allows the detection and analysis of spike bursts. The spikes have to be detected by the spike sorter first. The quality of the burst analysis therefore depends heavily on the accuracy of the spike detection. Add the "Spike Sorter" and the "Spike Analyzer" to the virtual rack. Click "Analyzer" tab. Spike burst analysis will be active as soon as the "Burst Marker" is selected. Bursts are detected based on the MaxInterval Method.
MC_Rack Manual The detection parameter for bursts are shown in the following picture. Parameter for burst detection: Max. interval to start bursts: maximum interspike interval to start the burst. Max. interval to end a burst: maximum interspike interval to end the burst. Min. interval between bursts: minimum interspike interval between two bursts. Min. duration of burst: minimum burst duration. Min. number of spikes in burst: minimum number of spikes in a burst. (Reference: Legendy C.R. and Salcman M.
MC_Rack Features Different units on each electrode, separated by the spike sorter, will be shown in different colors. In the same window, a color coded line under the time stamps will mark the detected bursts individually for each unit. Unit 0 represents all unsorted spikes together, and is displayed in green as shown in the picture above. Online Detection of Spike Burst Parameters Click in "Spike Analyzer" the "Analyzer" tab. The "Burst Detection" dialog allows setting the parameters described above.
MC_Rack Manual 1. Channel / Unit 2. Number of Spikes 3. Mean Spike Frequency [Hz] 4. Number of Bursts 5. Bursts per Second 6. Bursts per Minute 7. % of Spikes in Burst 8. Mean Burst Duration [ms] 9. Mean Spikes in Burst 10. Mean ISI in Burst [ms] 11. Mean Spike Frequency in Burst [Hz] 12. Mean Interburst Interval [ms] Hint: All parameters will be calculated, independently from the selected online burst parameters.
MC_Rack Features Add a display to your virtual rack. Click “Data” tab. In “Data Streams” select “Spike parameter 1” and “Timestamp”. In “Plot Type” please select check box “Trace”. Start the recording or replaying. Zoom into one channel on the display by double click. You see the timestamps only. Click icon to export the timestamp data to one single data file or to export them to one file per channel.
MC_Rack Manual 4.14 Analyzing Data 4.14.1 Analyzing Data Two virtual instruments are provided for data analysis: Standard Analyzer based on discrete time intervals (bins or region of interest) for general analyzing purposes (all data streams supported). This Analyzer type is especially useful for waveform analysis, for example, for amplitude and slope analysis of evoked responses. Extracted parameters can be graphed in the Parameter Display.
MC_Rack Features 4.14.2 Time-Interval Based Analyzer Extracted Parameters The following parameters can be extracted with the Analyzer from the described data streams.
MC_Rack Manual Slope extraction The 10 % / 90 % (or 20 / 80 or 30 / 70) interval of the peak-peak amplitude (stretching from minimum to maximum) in the region of interest is detected. Only data points in this interval are used for the linear regression fit (Least Square Algorithm). The slope of the resulting straight line (not shown in the Analyzer) is extracted as the slope. Triggered Mode vs. Continuous Mode The Analyzer can be operated either synchronized on a trigger event, or continuously.
MC_Rack Features 1. Set up a rack with a Trigger Detector and an Analyzer. 2. Click the ROI tab of the Analyzer. 3. Select the option Start on Trigger and choose the appropriate trigger from the drop-down list. The Analyzer display appears. You can change the layout of the Analyzer display in the same way as that of a standard display. 4.
MC_Rack Manual Maximum trigger rate Please note that the ROI must be defined in a way that the trigger rate does not cause ROIs to overlap. The maximum refresh rate of the Analyzer display is determined by the x axis range selected from the drop-down list on the display toolbar. In contrast, the Analyzer functionality, that is, the parameter extraction, is directly related to the trigger events, not to the display.
MC_Rack Features When monitoring faster signals like neuronal spikes, a bin size of 1 s will generally be fine. For special applications, it can make sense to use a smaller bin size, that is, if you are interested more in the organization of signals than in the overall spike rate. For example, if the Analyzer extracts the spike number in 100 ms bins, you will get a pattern of empty and non-empty bins (with a majority of empty bins) if the spike pattern is highly organized in bursts.
MC_Rack Manual 4.14.3 Event-Based Spike Analyzer Extracted Parameters (Spike Analyzer) The following parameters can be extracted with the Spike Analyzer. Only Spike data streams are available as input streams. Each detection event generates a data point. Interspike Interval Time interval between detection events (as detected by the Spike Sorter) Rate Event rate in Hz (1 divided by the interspike interval) Timestamp Indicates a detected spike at a that time, when the spike occurs 4.
MC_Rack Features 4.15.3 False Color Maps In the Color vs. Time and the False Color plot, color values or gray-scale intensities are assigned to parameter values. The colors are chosen from a Color Map. The following pre-set color maps are available: Jet, Hot, Cool, Gray and Jet reverse. Each color map consists of 64 different colors arranged in a particular way.
MC_Rack Manual You can choose between four different false color maps. The False Color plot shows only the current values as colors without information about the time. Each parameter value is assigned to one of 64 colors (defined by the Color Map). There is no time axis, the plot is refreshed according to the Window settings of the Analyzer. Scrolling back and forward is not available for this plot type, but will be enabled in future versions. The scroll arrows are present but inactive.
MC_Rack Features 4.15.7 Parameter/Digital Display Tools + Settings Each Parameter Display or Digital Display has a toolbar at the top of the window. Zoomed Channel: This icon appears, when you have zoomed a single channel. Apply to All: (In zoom mode) Applies the display settings to all channels. Show/Hide Measure Tool: A vertical bar in the color of the data channel is shown that displays the x- and y-value of the intersection point. You can position the bar with the mouse.
MC_Rack Manual Note: In general, all buttons apply only to the displayed channels. If, for example, 64 channels are displayed, moving and zooming of the axes will apply to all channels. If, on the other hand, a single channel was zoomed to it's full size by double-clicking it, all toolbar buttons would correspond only to this particular channel. You can apply the settings to all channels by clicking the Apply to All button.
MC_Rack Features Move the mouse pointer over the clamp control cursor / measure tool until the mouse pointer becomes a hand and then press the right mouse button to show the options. Channel Switch between the y value channels. See the Data tabbed page of the Spike Parameter display for available channels. Style Value x-y Default option. Label shows x and y values of intersection point. Value x Label shows only x value of intersection point.
MC_Rack Manual 4.15.8 ASCII Export of Extracted Parameters Click to save the complete data streams of the displayed channels as a tab-delimited ASCII file (text without formatting). You may then send this data to an editor or to your custom analyzing software, for example. ASCII export is possible with all four parameter plot types. Exporting data is only possible when you have stopped the data acquisition / Replayer. The Save button will then reappear on the toolbar.
MC_Rack Features 4.16 Averager 4.16.1 Averaging Data Sweeps The Averager adds up triggered sweeps successively. You can use the Averager to reduce the noise level and to enhance your signals, for example, to detect field potentials or for evoked potential analysis. Noise usually stems from arbitrary signals, where "real" signals should follow a pattern, that is, the signal event is linked to a stimulus or a trigger signal.
MC_Rack Manual Note: When recording averaged data, you can save the data only continuously. The averaged data stream is recorded "triggered", that means, only the last sweep of the set sweep numbers is saved. For example, if you set the sweep number to 100, every 100th averaged sweep is saved. If you stop the recording or restart the Averager before the last sweep has been reached, no data will be saved at all. 4.17 Sound Output 4.17.
MC_Rack Features 4.17.2 Audio Out with USB-ME Data Acquisition Using an USB-ME device you can additionally transfer electrode activity into sound with the "Audio Tool" feature. You can convert signals from one channel into mono sound, and signals from two channels into stereo sound. In contrast to the sound audible with the usual "Sound" output, the sound of the signals generated with "Audio Tool" are in real time. The sound is audible during data acquisition.
5 Data Export 5.1 About Data Export The data acquisition and analysis program from Multi Channel Systems MC_Rack provides tools for a user friendly online and offline analysis of basic parameters like peak-to-peak amplitudes, spike rates, and so on. For more advanced analysis methods like tetrode analysis, or analyzing sorted spikes, you can easily transfer your data files to external analysis programs. Several free or commercially available programs support data files generated with MC_Rack (*.
MC_Rack Manual Spike2 CED .mcd (MC_Rack) Spikes, field potentials Analysis, for example spike sorting, PSTH, correlational analyses, filters, tetrode analysis, waveform analysis NeuroExplorer Nex Technologies .mcd (MC_Rack) Spikes, event data Statistical analysis, for example PSTH, correlational analyses, histograms, rasters, activity graphs and maps, interspike intervals, burst analysis, principal component analysis CMC Tools University Freiburg .
Data Export 5.2 Graphs for Presentations 5.2.1 Low Resolution Pics (Screen Shots) You can use the Image Capture feature of the Parameter Display for a basic picture of the displayed channels. If you want to make a screen shot of the complete program window, you can use the built-in snapshot feature of the Windows operating system (press ALT + PRINT SCREEN for copying the active program window or PRINT SCREEN alone for the complete screen content).
MC_Rack Manual You can also use the commercially available program DataAccess Pro from Bruxton (www.bruxton.com) to open * .mcd files directly and import data streams into several scientific graphing and analysis programs. 5.3 Extracting Spikes 5.3.1 Spike Sorting MeaTools and Matlab for data recorded from MEAs Prof. Dr. Ulrich Egert from the university in Freiburg, Germany, has designed the MEATools (www.brainworks.uni-freiburg.
Data Export Spike2 automatically creates templates from raw spike data based on user-defined parameters. Spike2 can cluster spike data using principle component analysis or user-defined spike waveform measurements. Clusters can be formed automatically with the K-means algorithm or by cutting clusters manually using ellipses. 3-D rotation of clusters and replay of activity enables better viewing of cluster formations. Spike2 allows to open *.mcd files directly. 5.3.
MC_Rack Manual 5.4.2 Waveform Shape and QT Interval For drug screenings, the analysis of the waveform, especially of the field potential duration, is of main interest. The field potential duration corresponds to the action potential duration, that is, the QT interval in an electrocardiogram. It is generally measured from minimum of the Na+ peak to the maximum / minimum of the IKr current peak. Matlab based Cardiomyocyte Toolbox (CMC Tools) This toolbox programmed by Prof. Dr. Ulrich Egert (www.brainworks.
6 Troubleshooting 6.1 Technical Support Please read the Troubleshooting part of the MC_Rack Manual / Help first. Most problems are caused by minor handling errors. Contact your local retailer immediately if the cause of trouble remains unclear. Please understand that information on your hardware and software configuration is necessary to analyze and finally solve the problem you encounter.
MC_Rack Manual 6.2 Error Messages 6.2.1 Computer Performance Performance limit messages occur if the computer performance does not support the current rack configuration. The more virtual instruments (especially displays and digital filters) you use, the higher is the CPU usage. Open the Windows Task Manager and watch the CPU usage. Try the following. Do not run any programs (especially no virus scanning program or firewall) in parallel on the data acquisition computer.
Troubleshooting 6.2.2 Replayer Occurs when a rack file is opened and the file path of the data file loaded into the Replayer is not valid. The Open dialog box will open automatically. Please select an appropriate data file (*.mcd) and click Open. The file name of the file that was loaded into the Replayer will be suggested to you.
MC_Rack Manual 6.2.3 Recorder Occurs when the "Window Extent" setting in "Windows" tab of the Recorder is out of range. Please read chapter "Triggering MC_Rack on a Stimulus" for more information about "Window Extent" settings. 6.2.4 Running more than one instance of MC_Rack in parallel When using more than one instance of MC_Rack in parallel an error message will be displayed if the user tries to open more than the defined numbers of instances of MC_Rack. 6.2.
Troubleshooting 6.3 Data is not Written to Hard Disk You started the recording by pressing the Start button. You see the recorded data in the MC_Rack displays, but no data is written to the hard disk. Possible causes: ? The red Record button was not pressed in. MC_Rack was designed like a tape deck.
MC_Rack Manual Signals on the analog channels are recorded "as is", with no respect to the gain specified in MC_Rack, as the true gain is generally completely different on the electrode inputs and on the additional analog inputs. Therefore, you generally need different y-axis ranges (and therefore separate displays) for seeing the data traces in an appropriate scale.
Troubleshooting 7 Appendix 7.1 Contact Information Local retailer Please see the list of official MCS distributors on the MCS web site. User forum The Multi Channel Systems User Forum provides the opportunity for you to exchange your experience or thoughts with other users worldwide. Mailing list If you have subscribed to the Mailing List, you will be automatically informed about new software releases, upcoming events, and other news on the product line.
8 Glossary A aliasing: Frequencies (noise) that are above half the sampling rate (for example above 2.5 kHz at a 5 kHz sampling rate) will be transformed into lower frequencies. anti-aliasing: Using an analog Low Pass filter for removing high frequency noise, which would lead to aliasing if a sampling frequency lower than twice the bandwidth of the input signal is used.
MC_Rack Manual E Enhanced Meta File (EMF): Intermediate format for exchanging vector graphics data, file extension *.emf EPSP: Excitatory postsynaptic potential, an electrical change (depolarisation) in the membrane of a postsynaptic neuron caused by the binding of an excitatory neurotransmitter from a presynaptic cell to a postsynaptic receptor.
Glossary O OTC: Organotypic Culture: An MEA experiment where the slice is cultured on the MEA for weeks or months, in contrast to an acute slice experiment. P peak-peak: Interval from maximum to minimum signal PPD: Paired Pulse Depression PPF: Paired Pulse Facilitation R Real-time Feedback: The real-time feature allows the user to generate TTL signals in response to defined signal patterns detected by one or several electrodes.
9 Index 187
MC_Rack Manual 188
recording averaged data ................. 99 replaying averaged data.................. 99 1 1-dimensional data source setup..............................73 2 2-dimensional data source setup..............................73 A Add Digital Output Advanced Configuration Aliasing 130 23 154 Analog Raw Data about .................................................95 additional analog channel ...............23 averaging.........................................185 detecting triggers ...........................
MC_Rack Manual Longterm Display ..............................36 plot types.........................................118 settings ............................................112 Data export about ................................................. 95 analyzing......................................... 172 averaging ........................................ 185 displaying ........................................ 118 filtering ........................................... 146 recording..............................
for presentations.............................190 high resolution................................191 Index masking digital input bits .............. 125 Matlab using MC_Rack files ........................ 191 Grouping Multitrode .........................................93 Maximal sampling frequecy Guided Tour Maximum 7 H Hardware data source setup..............................73 MC_Card settings ..............................88 High high pass filter.................................149 logical state .
MC_Rack Manual display refresh rate......................... 112 sampling............................................ 88 spike rate......................................... 173 O Offset defining a channel offset in channel maps for non-rectangular grids .....111 Offset Correction On Trigger 88 105 Oscilloscope Data Display ....................................118 Digital Display .................................121 display types ....................................110 Parameter Display ...................
Index File Source .........................................93 Sine Waves Simulation mode...............................93 Synchronize recording......................................... 105 SyncOut 125 Slope analyzing slope ...............................173 spike detection (slope) ...................163 spike detection (threshold) ............162 trigger detection.............................127 T Snapshot Threshold spike detection ............................... 162 trigger detection ................
MC_Rack Manual W8-System 33, 73 Wait automatic trigger............................129 White display background color ...............112 Window spike sorting ....................................165 194 time window............................. 98, 173 Window Extent ........................... 47, 98 Wireless Recording System 33, 73 Wireless System Wireless System W4 .......................... 70 Wireless System W8 ..........................
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