Multichannel Systems MC-Rack User Manual

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. In no event shall the publisher and the author be liable for any loss of profit or any other commercial damage caused or alleged to have been caused directly or indirectly by this document.

Printed: 09. 09. 2013

Multi Channel Systems

MCS GmbH

Aspenhaustraße 21

72770 Reutlingen

Germany

Fon +49-71 21-90 92 5 - 0

Fax +49-71 21-90 92 5 -11

info@multichannelsystems.com

www.multichannelsystems.com

Microsoft and Windows are registered trademarks of Microsoft Corporation. Products that are referred to in this document may be either trademarks and/or registered trademarks of their respective holders and should be noted as such. The publisher and the author make no claim to these trademark.

Table of Contents

Introduction 1

About this Manual 1 Terms of Use 2 Limitation of Liability 2 Important Safety Advice 2

First Use of MC_Rack 3

Welcome to MC_Rack 3 Installing MC_Rack 4

Step by Step Tutorial 7

Using the Step by Step Tutorial 7 Monitoring and Recording Activity 8

Starting MC_Rack 8 Defining the Data Source 9 Advanced Configuration 24 Adding a Data Source 32 Channel Tool 35 Monitoring Activity Continuously 36 Recording Data 42 Starting Data Acquisition and Recording 44

Monitoring and Recording Triggered Activity 45

Triggering MC_Rack on the Stimulus 45 Monitoring Triggered Activity 47 Recording Triggered Data 48

MEA2100-System 51

Wireless-System 64

Wireless System 64

MC_Rack Features 67

About MC_Rack Features 67 Data Acquisition Settings 67

Data Source Setup 67 Defining Hardware Settings 83 Channel Tool 86 Grouping Multitrode Channels 87 Simulation Mode 87

Data Streams and Channels 90

Data Stream Types 90 Channel Selection 91 Continuous and Triggered Data 92 Averaged Data 94 Digital Data and Binary Code 96

iii

MC_Rack Manual

Recorder 97

Replayer 101

Displaying Data 104

Data Display (for Monitoring Raw Data) 111

Digital Display (for Monitoring TTL Inputs) 114

Trigger Detector 115

Automatic Feedback 122

Real-time Feedback 123

Filtering Data 134

Spike Sorter 142

Analyzing Data 152

Recording Data 97 Generating Data Files 99

Loading a Data File 101 File Specifications 102 Replaying Data 102

Display Types 104 Setting up a Display Layout 104 Display Settings 106 Peak Detection 107 Customizing a Display 109 Displaying a Background Picture 109 ASCII Export of Waveforms 110

Plot Types 111 Trace Plot 111 Overlay Plot 111 Raster Plot 112

Displaying Digital Data 114 Numeric Display 114

Using the Manual Trigger 115 Triggering MC_Rack 117 Triggering on TTL Pulses 117 Triggering on Biological Signals 119 Triggering on Extracted Parameters 120 Time Based Trigger 120

Digital Output 122

Real-time Feedback 123

Filtering Data 134 Filter Characteristics 137 Filtering and Sampling Rate 138 Downsampling 140

Spike Detection Methods 142 Detecting Spikes by a Threshold 143 Detecting Spikes by Waveform 143 Spike Cutouts 144 Spike Sorting 145 Burst Analysis 147

Analyzing Data 152 Time-Interval Based Analyzer 153 Event-Based Spike Analyzer 158

Table of Contents

Parameter + Spike Analyzer Display 158

Plot Types 158 Trace Plot 158 False Color Maps 159 False Color vs. Time (Plot) 159 False Color Plot 159 Number Plot 160 Parameter/Digital Display Tools + Settings 161 ASCII Export of Extracted Parameters 164 Image Capture 164

Averager 165

Averaging Data Sweeps 165

Sound Output 166

Sound Output with MC_Card 166 Audio Out with USB-ME Data Acquisition 167

Data Export 169

About Data Export 169 Graphs for Presentations 171

Low Resolution Pics (Screen Shots) 171 Working with Graphics Programs 171

Extracting Spikes 172

Spike Sorting 172 General Spike Analysis 173

Analyzing Cardiac Signals 173

Wave Propagation 173 Waveform Shape and QT Interval 174

Extracting Parameters 174

Exporting Parameter Streams to Excel 174

MC_DataTool 174

About MC_DataTool 174

Troubleshooting 175

Technical Support 175 Error Messages 176

Computer Performance 176 Replayer 177 Recorder 178 Running more than one instance of MC_Rack in parallel178

Hardware Errors 178 Data is not Written to Hard Disk 179 Channels Not Visible or Available 179

Appendix 184

Glossary 183

Index 187

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. We suggest that you start MC_Rack and then follow the Guided Tour step by step, either using the integrated Help or the printed manual. Just decide what you like to do, read all necessary information in short and put this information directly into practice.

If you need further information or like to review specific topics as an already experienced user, please confer to the "MC_Rack Features" part, where you can find more precise information about all topics.

The printed manual and Help are basically the same, so it is up to you which one you will use. The Help offers you the advantage of scrolling through the text in a non-linear fashion, picking up all information you need, especially if you use the Index, and the Search function. If you are going to read larger text passages, however, you may prefer the printed manual.

The device and the software are part of an ongoing developmental process. Please understand that the provided documentation is not always up to date. The latest information can be found in the Help.

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.

To the maximum extent permitted by applicable law, in no event shall Multi Channel Systems MCS GmbH or its suppliers be liable for any special, incidental, indirect, or consequential damages whatsoever (including, without limitation, injuries, damages for data loss, loss of business profits, business interruption, loss of business information, or any other pecuniary loss) arising out of the use of or inability to use MC_Rack or the provision of or failure to provide Support Services, even if Multi Channel Systems MCS GmbH has been advised of the possibility of such damages.

1.4 Important Safety Advice

Warning: Make sure to read the following advices prior to install or to use MC_Rack. If you do not fulfill all requirements stated below, this may lead to malfunctions or breakage of connected hardware, or even fatal injuries. Obey always the rules of local regulations and laws. Only qualified personnel should be allowed to perform laboratory work. Work according to good laboratory practice to obtain best results and to minimize risks. Make always sure to validate your findings. Prepare backup copies on a regular basis to avoid data loss.

 The operator is obliged to ensure that MC_Rack is only be used for its intended purpose and that

it is only used by qualified personnel.

 MC_Rack is not intended for medical uses and must not be used on humans, especially not for

uses that could impair health.

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. It has been developed especially for use with the (USB-) ME- and the (USB-) MEA-System, but is also ideally suited to work with other experimental setups.

Together with the data acquisition device, MC_Rack fully replaces a complete hardware set for data acquisition. For example, you do not need an oscilloscope, a filter, or a spike detector device anymore, because all this functions are integral part of the software. You set up a virtual instrument rack, which is comfortable, easy to use, and saves space on your workbench.

The main power of MC_Rack is its great flexibility. You can combine various virtual instruments according to your experimental setup. You can decide about the fate of each single data stream separately. It is up to you, which data streams are displayed on the screen, which are saved, which are analyzed, and so on. This concept saves disk space and computer performance and makes handling of up to 256 channels with up to 50 kHz sampling rate easy. A status bar informs you on the actual performance of your computer when you record or replay data.

Please note that the high flexibility of MC_Rack makes a complex configuration of the software necessary. As a fresh user of MC_Rack, this may present some difficulties to you. But the straightforward user interface will soon make you feel comfortable with the general concept and learn to appreciate the advantages of the system. This documentation tries to help you on your way.

It is very important to note, that all virtual instruments in your rack work independently from each other. As a consequence, they have to be configured separately. For example, you have to select the input streams for each instrument separately.

Generally, you will arrange the virtual instruments in your rack in a hierarchical order. The selected data streams flow from your data acquisition or from the Replayer (recorded data) into the virtual instrument highest in the hierarchy. Similar to a production line in a plant, this instrument picks up only those channels from the data streams that you have assigned to it. It processes this data and produces an output stream, that is lead to the virtual instrument(s) next in the hierarchy, and so on. When you build a rack, make yourself clear, which data streams flow to which instrument and what output you should expect. If you change the selection of channels for a virtual instrument, you may have to adjust the selection for instruments that depend on its output as well. If you have not specified an input for a tool, an error message will inform you.

In MC_Rack, the rack you use to record and analyze data online and offline, and the data files are as a matter of principle independent from each other. You can save and reuse a rack for several experiments and generate separate data files. You can then load the generated data file with another rack for further offline analysis later.

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. We recommend to study especially the applications that you are interested in before starting an experiment, so that you learn about the possibilities and how to configure MC_Rack for different applications. This section is more detailed than the tutorial. Also, it is easier to understand the software features when playing around with demo data.

 MC_Rack Features: All MC_Rack features are explained in detail. This section is especially useful

if you want to learn more about a specific software feature.

 Data Export: Summarizes the export options of MC_Rack and MC_DataTool and provides

recommendations for third party programs for offline data analysis.

 Troubleshooting: Lists typical minor problems that might occur during operation and gives hints

how to solve them.

2.2 Installing MC_Rack

The data acquisition computer with the data acquisition device, for example MC_Card or USBMEA256, comes preinstalled and preconfigured by MCS for a flawless operation. You should contact your local retailer for assistance if you want to install additional hard- or software, or if you want to replace the computer, as incompatibilities of hardware components or software settings with MC_Rack may occur.

Caution: You have acquired a high performance data acquisition and analysis computer. Do not modify the system, do not install new hard- or software, or another operating system without asking MCS or your local retailer for advice. Especially do not install virus scanners or firewalls because these programs are known to interfere with the data transfer to the hard disk. MCS cannot guarantee that a modified system is fully operational. Even data loss may occur.

System requirements

Software:

One of the following Microsoft Windows ® operating systems is required: Windows 7, Vista, or XP (English and German versions supported) with the NT file system (NTFS). Other language versions may lead to software errors.

Hardware:

The data acquisition board MC_Card. (Not required for offline analysis or demo mode). If no MC_Card is present, MC_Rack opens in a simulation mode. A computer with low performance may lead to performance limits more often; therefore, MCS recommends an up-to-date computer. Please note that there are sometimes hardware incompatibilities of the MC_Card and computer components; or that an inappropriate computer power supply may lead to artifact signals. Please contact your local retailer for more information on recommended computer hardware.

The USB-ME-Systems or the USB-MEA-Systems. (Not required for offline analysis or demo mode). The USB based data acquisition systems do not need the MC_Card. These systems are equipped with an internal data acquisition. The analog input signals from up to 256 channels are acquired and digitized by the systems and the digital electrode signals are transmitted to the connected computer via universal serial bus (High Speed USB 2.0).

Important: You need to have installed the latest driver to operate the data acquisition device, which is automatically installed with MC_Rack. The installation may be invalid if the data acquisition device does not respond. Please contact Multi Channel Systems or your local retailer in this case.

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.

 Optimize hard disk when idle (automatic disk fragmentation) turn off.

 It is also not recommended to run any applications in the background when using MC_Rack.

Remove all applications from the Autostart folder.

 Be careful when using a Virus Scanner. These programs are known to disturb MC_Rack,

and even data loss may occur.

 When using an USB-ME-System or an USB-MEA-System it is recommended to connect

a high performance computer with a separate hard discs for program files and data storage. The provided possibility to use up to 256 channels with a sample rate of up to 40 kHz needs high memory capacity. Please remove data and defragment the hard disc regularly to ensure optimal performance.

Warning: The operating system settings of the data acquisition computer were preconfigured by MCS and should not be changed by the user. Changing these settings can lead to program instabilities and data loss.

Switching on the connected computer

(Applicable only if you use a data acquisition computer from Multi Channel Systems.)

1. Power up the connected computer and wait until it is ready. The Login dialog box appears.

2. Enter "mcs" both as the user name and as the user password. You do not have to enter an

administrator password. (You may change the passwords later, of course.) The Windows desktop is displayed.

Installing the software

Please check the system requirements before you install the software. MCS cannot guarantee that the software works properly if these requirements are not fulfilled.

Important: Please make sure that you have full control over your computer as an administrator. Otherwise, it is possible that the installed software does not work properly.

1. Double-click Setup.exe on the installation volume. The installation assistant will show up

and guide you through the installation procedure.

2. Follow the instructions of the installation assistant. The hardware driver and MC_Rack are installed (or updated) automatically.

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. So, if you prefer to start with a preconfigured rack, you can load the rack of interest first, and then go through this tutorial to see how to adapt the rack's settings and parameters to your needs, but we recommend that you take a bit time to build it yourself to learn the principle of operation.

Both racks discussed in the Step by Step Tutorial are basic racks for monitoring and recording data. The only difference is, that Monitoring and Recording Activity Continuously describes how to monitor and record activity continuously (generally used for spontaneous activity). Monitoring and Recording Triggered Activity describes how to monitor and record activity triggered by an event, that is, for evoked responses, for example, in an LTP experiment. All important information is repeated in each section, so you may freely choose the rack that is suitable for your application without missing information.

The difference to the MEA application examples (see separate document) is that the racks that we set up in this tutorial can be used directly in a real experiment. Without demo data, they may appear somehow a bit abstract. If you are new to the extracellular recording technique and want to get an impression how MC_Rack works and how signals can look like, you may prefer to have a look at the MEA application examples and demo racks first. Also, in the MEA application examples section, more advanced MC_Rack features are explained in detail and very near to the application.

You will find a list and a short description of all sample racks in the MC_Rack Sample Racks topic.

The MEA Signal Generator

The MEA Signal Generator MEA–SG is a convenient tool for MEA-Systems first time users. The device has the same dimensions and connector layout as a 60-channel MEA chip and is compatible with all MEA1060 amplifier types and with the MEA2100-60 / MEA2100-2x60-Systems. The MEA–SG can produce sine waves, or replay a variety of biological signals. These signals are fed into the MEA amplifier as analog signals. With this artificial data, you are able to test the functionality of the hardware and software system, without the need for a biological sample. Please use the 256MEA-SG for the USB-MEA256-System and the 120MEA-SG for MEA2100-120Systems..

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. You will learn in this tutorial how to set up racks for some typical applications.

MC_Rack main window (empty)

The virtual rack

The title bar shows the file name of the virtual rack (the default name before saving the rack under a custom name is Rack1). The white pane on the left of the virtual rack window holds the virtual rack tree view pane, where all virtual instruments that are part of this rack are represented by icons and (customizable) individual instrument names.

After program start, the virtual rack is almost empty, it holds only a single virtual instrument the Recorder, represented by a small cassette player icon. The context-sensitive grey pane on the right shows the virtual instrument settings (organized in tab pages) of the virtual instrument that is selected (highlighted in blue) in the virtual rack tree view pane on the left. If you have added more instruments to the rack, you were able to click through the instruments in the tree view pane, and click the tabbed pages to review or change any settings.

At this point, only the Recorder settings are available. The first Rack tabbed page is always the same for all virtual instruments here, you can start and stop MC_Rack (that is, the data acquisition or the Replayer), and activate the recording (that is, writing data to hard disk).

The Lag status bar gives you information on the computer performance; the lower the Lag, the better the performance. When the Lag exceeds the maximum, MC_Rack will be stopped automatically, and you will be informed about a performance limit of the computer by an error message. The complexity limit of the virtual rack depends directly on the computer performance. To avoid data loss during over night recordings, for example, test the rack configuration thoroughly under realistic conditions (that is, the signal rate should be as expected in the real experiment) before starting the experiment. If you have trouble with the computer performance, please see the chapter Error Messages in the Troubleshooting section for more information on how to optimize the rack configuration.

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. Please check the disk space and estimate how long you still can write data to the hard disk always before starting an experiment. Otherwise, data loss will occur when the disk is full. For example, if you record 60 electrode channels at a sampling frequency of 25 kHz, the data rate is 3 MB/s, that is

10.8 GB/h.

MC_Rack toolbar. For a more detailed information on the toolbar buttons, please see "Toolbar" under General User Interface.

The MC_Rack toolbar shows all main functions available in MC_Rack. You can click on a virtual instrument button to insert a virtual instrument into your rack configuration. Please note that virtual instruments that need an input data stream that is generated by another virtual instrument (for example, the Spike Analyzer, which needs a Spike data stream generated by the Spike Sorter) can only be placed in series with the required virtual instrument and are otherwise not available (indicated by a gray button color). In an empty rack, only the data source, that is, the data acquisition or the replayer, are available to start with. After the data source was inserted into the rack, other virtual instruments will be available.

3.2.2 Defining the Data Source

MC_Rack is the universal data analysis program for all ME- and MEA-Systems with PCI card as well as with USB based data acquisition. To ensure correct display of the data of your system, it is therefore necessary to configure the data source accordingly. This has to be done only once for a given rack. See the MEA-System manual or the ME-System manual for the MC_Rack features that are supported by your system.

On the Edit menu, click Data Source Setup to configure the software according to your data acquisition and amplifier hardware. Data Source Setup is only available as long as no data source is included in a new rack file. Configure the channel layout first and then set up the rack for your experiment. The data source setup and channel layout information is saved together with the rack.

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). A digital IN / OUT extension is available that supports all 16 digital in- and output bits.

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. The standard BNC connectors for the digital channel on the data acquisition computer support only three digital input bits (0, 1, 2). A digital IN/OUT extension is available that supports all 16 digital in-and output bits.

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. For the electrode channels, the original signal is calculated automatically according to the gain settings in MC_Rack. Signals on the analog channels are recorded "as is", with no respect to the gain.

Deselect the option Digital Input Channel, if you do not want to use the digital input channel. One of the digital input bits can be used for triggering the recording on a TTL output of the stimulator, for example. A typical configuration of a ME64-System would be 63 electrodes and a digital channel. Please note that the use of the digital input channel is available on the cost of an analog channel, that is, if you have an ME16-System and want to use the digital channel, for example for synchronizing stimulation and recording, you could only use a maximum of 15 electrode channels. Make sure that you select the digital channel if you want to trigger the data analysis and/or the recording.

Hint: Deselect the option Digital Input Channel, if you do not need a digital channel. Otherwise the number of electrode recording channels is reduced by 1!

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. To configure the MEA layout, please use the right drop down menu "MEA". To configure the amplifier, please use the left drop down menu "Amp" (MEA1060 without blanking circuit, gain factor 1200, and MEA1060BC with blanking circuit, gain factor 1100 for MEA-Systems, and FA64I/S, FA32I/S for ME-Systems, MEA2100-H60 or MEA2100H120 for MEA2100-System).

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. The data source layout is 1 dimensional, with 16 electrode channels, and an additional digital channel.

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. The data source layout is 1 dimensional, with 32 electrode channels, and an additional digital channel.

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. The USB MEA device will be specified on the right Data Source drop down menu: USB-ME256 (S/N: 0004). The number in brackets is the serial number of the device. Adjust the number of channels available.

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. Number of MC_Rack Instances = 4" in Advanced Configuration you can control each of the four amplifiers independent from the others with its own MC_Rack software.

Note: Setting up the configuration of the data source is important for having the correct layouts for MEA A, B, C and D during the complete experiment.

USB-ME128 Data Acquisition

The USB-ME128 device is in principle the same device as the USB-ME256, except for the total number of channels, that is 128.

The USB-ME128 is an external data acquisition device that uses USB 2.0 connection to transfer digitized data to any connected computer. Please see USB-ME128 Manual for detailed information. Select USB MEA from the Data Source drop down list. The USB MEA device will be specified on the right Data Source drop down menu: USB-ME128 (S/N: 0002), for example. The number in brackets is the serial number of the device.

In USB-ME128-System it is possible to configure two MEA1060 / MEA1060BC amplifiers independent of each other. Additionally it is possible to configure the MEA layouts for MEA A and MEA B independent of each other.

On the Edit menu, click Advanced Configuration to configure the software according to the USB-ME128 hardware. 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-ME128 with two MEA1060 amplifiers. With setting "Max. Number of MC_Rack Instances = 2" in Advanced Configuration you can control each of the two amplifiers independent from the other with its own MC_Rack software.

Note: Setting up the configuration of the data source is important for having the correct layouts for MEA A and B during the complete experiment.

USB-ME64 Data Acquisition

The USB-ME64 device is in principle the same device as the USB-ME256, except for the total number of channels, that is 64.

The USB-ME64 is an external data acquisition device that uses USB 2.0 connection to transfer digitized data to any connected computer. Please see USB-ME64 Manual for detailed information. Select USB MEA from the Data Source drop down list. The USB MEA device will be specified on the right Data Source drop down menu: USB-ME64 (S/N: 0002), for example. The number in brackets is the serial number of the device.

In USB-ME64-System it is possible to configure the MEA1060 / MEA1060BC amplifier. Additionally it is possible to configure the layout of MEA A.

Note: Setting up the configuration of the data source is important for having the correct layout for MEA A during the complete experiment.

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. The wireless system device, W8 for example, will be specified on the right Data Source drop down menu: MCS WPA8 (S/N: 00001). The number in brackets is the serial number of the system. The data source layout is 1 dimensional, with 8 electrode channels and an additional digital channel.

Note: With all electrode channels, the maximum sampling rate for the 8-channel Wireless Recording System W8-System is 20 kHz. It is possible to increase the maximum sampling rate up to 40 kHz by deactivating at least four electrode channels. Please pay attention to the sampling rate respectively, when using the W4-, W16- or W32-System.

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. Please read also chapter "Data Source Setup" in "MEA2100-System".

Select USB MEA from the left Data Source drop down list. The MEA2100 device will be specified on the right Data Source drop down menu: MEA2100 (S/N: 0000-A).The number in brackets is the serial number of the system, the character A labels the connected headstage, A is the first headstage, B is the second headstage. It is possible to run up to two instances of MC_Rack per headstage. Please read chapter "Advanced Configuration". Specify the “Number of Channels” first: 32 electrode channels, when connecting one headstage with 32 recording and 12 stimulation electrodes (MEA2100-HS32), 64 when connecting one headstage with 60 channels (MEA2100HS60) or 128 electrode channels when connecting two headstages with 60 channels (MEA2100HS60) or one headstage with 120 channels (MEA2100-HS2x60 or MEA2100-HS120) to the interface board. Choose “Configuration” in the data source layout. Enable the check box for the digital input channels. Select the correct headstage in the “Amplifier” drop down menu and specify the type of MEA.

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". Click the Amplifier drop down menus on the left side to configure the "Amplifier". Additionally it is possible to configure the MEA layouts for up to two MEAs A and B independent of each other. Click the MEA drop down menus on the right side.

MEA2100-32-System

The MEA2100-32-System is a descendant of the MEA2100-System with the same functions except of the real-time feedback. Please read the MEA2100 Manual for detailed information. Select USB from the left Data Source drop down list. The MEA2100-32 device will be specified on the right Data Source drop down menu: MEA2100-32 (S/N: 00018-A). The number in brackets is the serial number of the device. The data source layout is Configuration, with 32 electrode channels. It does not matter whether you select the digital input channel or not.

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.

This feature is meant to be used with the new USB based data acquisition systems USB-ME256 and USB-ME128. When two or four amplifiers are connected to the data acquisition, it is possible to operate each amplifier independently with one instance of MC_Rack. It is also possible to operate 128 or 256 channels with one instance of MC_Rack, for example, when working with an USB-MEA256 amplifier and a MEA with 256 electrodes. See Data Source Setup for details on the configuration. Up to four instances of MC_Rack can be started in parallel.

If the option "Stop on Data Loss" is selected, the MC_Rack program stops recording if it encounters problems during recording of a file. An error message will be displayed in the status bar.

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. Virtual Device Configuration: Click 1 x 256 from the drop down list on the left. In Virtual Device Configuration drop down list on the right Block 1 (Channel 1...256) is displayed.

5. Source Layout: Choose Configuration in Source Layout and the total number of 256 from the drop down list in No. of Channels.

6. Configure the connected amplifiers and MEA layouts independently from each other from the available drop down menus.

The same proceeding is possible with USB-ME128 device. The total number of channel is reduced to 128 channels, respectively.

Important: If working with one instance of MC_Rack, data acquisition from all four amplifiers can only be started in parallel, and all data will be saved in the same file.

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. Connect an USB-ME256 device to the data acquisition computer. Start the first instance of MC_Rack. Click Edit: Advanced Configuration and define Max. Number of MC_Rack Instances = 4.

2. Click Edit: Data Source Setup and select USB MEA under Data Source. Choose 4 x 64 channels from the left drop down menu in Virtual Device Configuration, and Block 1 (Channel 1...64) from the right drop down menu. Block 1 corresponds with input A of the USB-ME256.

3. Configure the correct amplifier type and electrode layout for input A

4. Open the second instance of MC_Rack software program.

5. Click Edit: Data Source Setup and select Block 2 (Channel 65...128) from the right drop down menu. Block 2 corresponds with input B of the USB-ME256.

6. Configure the correct amplifier type and electrode layout for input B.

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. Block 4 corresponds with input D of the USB-ME256.

12. Configure the correct amplifier type and electrode layout for input D.

13. If you try to open a fifth instance of MC_Rack an error message will be displayed. Please see Troubleshooting.

Now you are able to operate the different blocks of 4 x 64 channels with independent MC_Rack instances, and with independent configured amplifiers and MEA layouts.

The same proceeding is possible with USB-ME128 device. The total number of channel is reduced to 128 channels and two blocks and inputs (A and B), respectively.

The Reuse of an existing Rack File with multiple Instances of MC_Rack

The reuse of an existing rack file with multiple instances of MC_Rack running on the same computer is explained, using the example of the USB-ME256-System. If you are working with an MEA2100-32-System, please operate in the same principle.

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. Before the selected file will open in the second instance of MC_Rack, you have to change the data source specification from the copied file. That is why the dialog " Channel Layout" in "Data Source Setup" will automatically appear again. Please choose the appropriate MEA amplifier via block number, assigned the second instance of MC_Rack.

4. Now the reused rack file will be opened in the second instance of MC_Rack. The data source used for the rack is shown in the blue header of the dialog and after the data source icon.

Note: Please do not miss one of the described steps when reusing an existing file! Otherwise you have to delete the rack and start the instance of MC_Rack again.

Repeat step 1 to 4 to open the third and fourth instance of MC_Rack with an existing file to control the amplifiers three and four.

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.

Important: It is not possible to connect one device with more than one instance of MC_Rack.

1. Start the first instance of MC_Rack.

2. Click Data Source Setup on the Edit menu. Select USB on the left drop down menu of the "Data Source", and MEA2100-32 on the right drop down menu. Please see chapter "Defining the Data Source". Select the block you want to control with the first instance of MC_Rack "Block" number.

3. Select Configuration in Source Layout. The total number of channels is 32 with an additional digital input channel or not.

4. Add MEA2100-32 (S/N 00018-A, headstage A), for example, as the data source to your virtual rack for the first instance of MC_Rack. The data source and its serial number are displayed in the blue header of the dialog of the "Rack" tab as well as on the left side of the display.

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.

Opening an existing Rack File with MEA2100-32-System 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: Start the second instance of MC_Rack.

1. Click "Open" in File menu. The dialog "Open Rack Files" appears. Select the desired rack file.

2. Before the selected file will open in the second instance of MC_Rack, you have to change the data source device specification from the copied file. That is why the dialog " Channel Layout" in "Data Source Setup" will automatically appear again.

3. Please choose the appropriate MEA2100-32 headstage via block number, assigned the second instance of MC_Rack.

4. Now the reused rack file will be opened in the second instance of MC_Rack. The data source used for the rack is shown in the header and after the data source icon.

Note: Please do not miss one of the described steps when reusing an existing file! Otherwise you have to delete the rack and start the instance of MC_Rack again.

Maximal Sampling Frequency

Usually, the maximal sampling frequency for MCS data acquisition systems is 50 kHz. However, when using some advanced features of the USB-ME256 and USB-ME128, some limitations apply.

The maximal sampling frequency that can be achieved with 256 channels is 40 kHz. This is possible when using the USB-ME256 with the "Virtual Device Configuration" 1 x 256 (Please see above). With the USB-ME128 and USB-ME256 it is also possible to split the data stream into 2 x 64 or 2 x 128 and 4 x 64 channels, respectively, again by using the "Virtual Device Configuration". These virtual machines can then be controlled independently by up to four instances of MC_Rack. However, splitting the data stream into several virtual devices consumes system performance. Therefore, the maximal sampling frequency is limited to 25 kHz when using the virtual device configuration 2 x 64 (USB-ME128) or 2 x 128 and 4 x 64 channels (USB-ME256).

The Additional Analog Channels A1 to A4

The devices USB-ME256, USB-ME128, USB-ME64 and USB-MEA256 are equipped with four additional analog channels A1 to A4. Please refer to the respective manuals.

The additional analog channels A1, A2, A3 and A4 are available in MC_Rack data display and in MC_Rack long term display.

Note: Because of the different scaling of electrode data channels and the additional analog channels, it is recommended to visualize the analog channels in a separate display.

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. (MEA): Three additional analog channels are available A1, A2, A3.

Source Layout Configuration: All four additional analog channels are available A1, A2, A3 and A4.

Visualizing the Additional Analog Channels

Click

to add a data display. On the left window pane of the dialog the data display appears, labeled ”Display 1”. Double click on "Display 1" to rename the display for discrimination of the analog and electrode displays.

In the "Data" tab, select "Analog Raw Data" only.

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.

Additional Analog Channels with Different Instances of MC_Rack

If you use the Advanced Configuration to run more than one instance of MC_Rack at once, the same four additional analog channels A1 to A4 can be displayed in any of these instances.

3.2.4 Adding a Data Source

In MC_Rack, the input data streams for the virtual rack can come from different data sources: From the data acquisition board MC_Card or from the Replayer, that is, from previously recorded data (*.mcd) files, or from USB based data acquisition systems like USB-ME256, USB-MEA256, USB-ME16-FAI or MEA2100-System.

Here, we want to acquire new data and choose, for example the MC_Card as data source.

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. When you select the MC_Card so that the name appears highlighted in blue, you see three tab pages on the right: The general Rack tabbed page, and the MC_Card specific Hardware and Info tabbed page. In the Hardware page, you can define the hardware related settings. The Info page shows the channel layout.

2. In the tree view pane of the virtual rack, select the MC_Card, click the Info tab, and check the

channel layout settings that you have defined in the last step. You cannot modify the settings anymore once you have added the MC_Card. If the settings are not appropriate, remove the MC_Card from the rack (by selecting the MC_Card In the tree view pane of the virtual rack and pressing DELETE), and go back to the last step "Defining the Data Source". The following screen shot shows the information on the standard layout for the MEA60-System.

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. Click Enter to enter the Amplifier Gain settings according to your hardware. The gain settings are used for scaling and displaying the signals properly. So if you specified a wrong gain, you would perceive wrong signal amplitudes leading to false documentation and results. The default settings are 1200 for the standard MEA1060 amplifier, and 1100 for the standard MEA1060-BC amplifier. The amplifier gain of the MEA2100-System is automatically set, depending on the version of the hardware. If you have a ME-System, you should enter the total gain of the amplifiers. For example, if you have a MPA8I (with a gain of 10) and a filter amplifier with a gain of 100, you have a total gain of 1000. Please check the technical specifications of the connected amplifier(s) and make sure that you enter an appropriate value.

5. Select an Input Voltage Range of Data Acquisition Board for the MC_Card from the drop- down list. For standard signals and a standard gain amplifier, the default input range of -819 to +819 will be fine. You need a higher input voltage range if your biological sample generates higher voltages, for example, cardiac signals from whole-heart preparations, and/or the amplifier gain is considerably higher. The lower the input voltage range, the higher is the voltage resolution. Please see also Defining MC_Card Settings in the MC_Rack Features section.

6. The Signal Voltage Range is calculated from the Input Voltage Range of the Data Acquisition Board divided through the Amplifier Gain Factor.

7. Select a Sampling Rate from the drop down list. For most applications, 25 kHz will be fine. Please see also Defining MC_Card Settings in the MC_Rack Features section.

8. An Offset Correction is generally not necessary. You may use it when you observe a disturbing voltage offset on the input channels. Or you may use it during testing the system with a test model probe. Make sure that there are no signals on the channels when using the offset correction. Click Offset Correction to activate the Offset Correction. Click Learn Offsets to perform an individual offset correction for each input channel. MC_Rack takes 100 ms of the recorded data in the moment when the button is pressed to calculate the DC offset. The mean of this 100 ms sweep is subtracted from the recorded data as long as the Offset Correction button is pressed. The individual offset values for each channel are saved in the local settings of the data acquisition computer and are only overwritten when you click Learn Offsets again. Make sure you press the Learn Offsets button only when you have no real input signals or irregular noise signals on the electrodes. To be on the safe side, connect a test model probe to the amplifier.

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. The voltage value of this reference electrode will be mathematically subtracted sample point per sample point from all electrode signals in the stream. For example, a low frequency noise on all electrodes will be eliminated this way.

Step by Step Tutorial

Note: Be careful to choose an electrode with noise only as reference electrode. If the reference electrode contains signals too, the value of the signals will be subtracted together with the noise value, and falsify the data.

Click the "Channel Tool" icon from the Edit menu. The following dialog appears. Click the "Channels" tab.

in the main window toolbar, or select "Channel Tool"

Select the data stream you want to apply the channel tool: Electrode Raw Data in this example. Select a "Reference electrode" from the "Reference electrode" drop down menu.

MC_Rack Manual

3.2.6 Monitoring Activity Continuously

Next, you need a Data Display for monitoring the ongoing activity continuously.

Click 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). When you have changed the channel map, the last used channel map is loaded automatically as the default.

For monitoring the ongoing activity continuously over a longer period, add the Longterm Display.

on the toolbar or click Add Data Display on the Edit menu to add a Data Display

Click Display to your virtual rack.

The Longterm Display shows analog raw data and electrode raw data. You can display data in a user defined time span from 1 second up to 60 minutes. The longterm display tool allows to observe the development of the signals over a longer period. The Longterm Display displays the channels in the layout of the Channel Map you have created or loaded. In the Longterm Display the adjustment of the x-axis is disabled, and you cannot zoom in. The peak detection is permanent selected (for more information please see chapter Peak Detection).

on the toolbar or click Add Longterm Display on the Edit menu to add a Longterm

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. The electrodes are labeled in relationship to their position in the electrode grid, respectively to their coordinates. The first number refers to the x-axis (column), the second number refers to the y-axis (row). The character refers to the MEA, MEA A in this case, that is important when using more than one MEA amplifier. .

2. To load a different Channel Map, click MCS Channel Maps or if the channel map is user defined, click User Channel Maps. You can use the Channel Map drop down menu or you browse your folders and open the MC_Rack program folder. In the Channel Maps folder, you will find a selection of standard layouts, for example, for different MEA types, layouts for the MEA120-System (8x8meaA.cmp and 8x8meaB.cmp for the two separate MEA amplifiers), and various other layouts for single electrode columns on a MEA, for example. Select an appropriate channel map and click Open. The MEA layout appears on he right side of the dialog box and the display shows the channels in the selected layout accordingly. .

3. For setting up a custom layout, enter the desired number of rows and columns. The layout grid displayed on the right is updated accordingly.

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.13 (in the middle of the first row) is bigger than the other electrodes. Click 13 in the electrode grid. Enlarge the electrode in the data display with X-Extend = 300 and Y-Extend = 200 by overwriting the 0 in the numeric updown box or clicking the arrow buttons.

5. To change the position of the electrode in the data display use X-Offset for moving it to the left (negative integer) and to the right (positive integer), and Y-Offset for moving it downward (positive integer) and upward (negative integer). The X- and Y-Offset has a range from -100 to +100. Overwrite the 0 in the numeric updown box or click the arrow buttons. The layout displayed on the data display is updated immediately.

6. The electrode referring to channel No. 23 is bigger as well. Do the same procedure to enlarge and move it as described in point 4 and 5. Repeat this procedure as often as necessary, and you are able to build your custom display layout.

If you have two amplifiers in your setup (MEA120 System), use Channel Offset to assign the custom layout to the correct data stream. Please read also next chapter Selecting data streams. Until today, it only makes sense to give 0 in Channel Offset for connecting the custom layout to Electrode Raw Data 1 or 64 for connecting the custom layout to Electrode Raw Data 2.

If you want to keep the custom layout for later use, click Save and enter a file name.

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). It may make more sense to display the additional analog channels in a separate display, though, because in most cases, the scale of the axes will not be appropriate for both the electrode data stream and the additional analog data stream. For monitoring the digital data stream, please use the Digital Display. The Data Display has an oscilloscope-like function. Therefore, only the Trace option is available. The Parameter Display for graphing extracted parameters provides more options.

Starting MC_Rack

 Click Start

(either on the Measurement menu, the toolbar, or the Rack tabbed page) to

start the data acquisition. Each virtual instrument in the rack starts to process the channels and data streams that were assigned to it, that is, the Trigger Detector detects events on the digital input channel and generates a trigger data stream that, in turn, triggers the display. The display is refreshed at each trigger event.

Refresh rate and 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 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.

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. Please be especially careful when configuring the Recorder to avoid data loss.

Selecting data streams and channels for recording

The fate of each single channel is independent from other channels. You can pick exactly the channels you like to save from all generated data streams. For example, you can decide to save only one channel of raw data, but the peak-to-peak amplitude results of all, or of a specific selection of channels.

Select the Recorder in the virtual rack tree view pane and then click the Channels tabbed page. On the white pane on the left of the Channels page, you see the data streams that are available with your data source settings, for example, the Analog Raw Data, Digital Data, and Electrode Raw Data streams for the MEA-System. (It does not matter whether you have really connected a device to the inputs, though.) If you have selected a channel layout without the digital input, the Digital Data stream will not be available, for example.

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. Only data from the selected channels will be saved to the hard disk.

Choosing the file name and path

1. Click the Recorder tab.

Step by Step Tutorial

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. The file name is extended by four digits, counting up, for example, LTP-Parameters0001.mcd, LTP-Parameters0002.mcd, and so on.

If you rather prefer that the recording is completely stopped when a file has reached the maximum size, please select the option Auto Stop. For information on more options, please see "Generating Data Files" in the MC_Rack Features section.

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). Please do not prolong the "Window Extent" time interval to more than 3800 ms. Please read chapter "Triggering MC_Rack on the Stimulus" for more information about "Window Extent" settings. For more information on continuous and triggered data, please see the chapter Continuous and Triggered Data in the "Step by Step Tutorial" section.

This option is only available if there is a trigger stream available, that is, a Trigger Detector in the rack.

3.2.8 Starting Data Acquisition and Recording

Now that you have completed the virtual rack, you are ready to start the rack.

 Click Start

to start the data acquisition. Each virtual instrument in your rack starts to process the channels and data streams that were assigned to it.

 Click first Record

electrodes selected in the Recorder is saved to the file and location specified in the Recorder.

 Click Stop

Warning: Only data of the channels and data streams that were selected in the Recorder are saved in your data file when you start a recording. Data is only saved to the hard disk when the red Record button is pressed in. Make always sure that you have selected all channels of interest, and that the Record button is active before starting an experiment to avoid data loss.

(either on the Measurement menu, the toolbar, or the Rack tabbed page)

and then Start to write data to the hard disk. The data from the

to stop the data acquisition.

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. You can upgrade the system with a digital IN / OUT expansion that supports all 16 digital input (and output) bits that are provided by the MC_Card. For more information, see the ME- or MEASystem manual.

Note: It is recommended to use the digital input port for feeding in TTL signals. The analog inputs are intended for analog signals, like patch clamp data, for example.

For triggering MC_Rack, we need to set up a Trigger Detector in the virtual rack. The trigger stream generated by the Trigger Detector can then be used for triggering Data Displays, Analyzers, and the Recorder.

See also the sample rack Display_Triggered.rck.

Step by Step Tutorial

1. Configure your stimulator to output a TTL pulse that is synchronized to the stimulus pattern. If you are using a Stimulus Generator (STG) from MCS, you can program a Sync Out channel.

2. Connect the TTL output to digital input bit 0 (the first BNC socket). If you are using a MEA-System, make sure not to confuse the digital inputs with the analog inputs.

3. Click

4. In the tree view pane of the virtual rack, select the Trigger Detector, and click the Trigger page.

on the MC_Rack toolbar to add a Trigger Detector to the virtual rack.

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. (If you had, for example, connected the TTL output to digital input bit 1, you would need to select 1 instead of 0, and mask all other bits.) You may want to change the dead time (the time after a trigger event where no following trigger event is accepted), for example, if you run a paired pulse protocol, and want to trigger MC_Rack only on the first stimulus pulse.

Click Recorder and select "Window" tab.

Important: The "Window Extent" is the total time of the cutout sweep. If you prolong the trigger in “Window Extent” to more than 3800 m, a Warning will pop up. MC_Rack will record data, but you cannot display these data when replaying them, because the MC_Rack display setting for displaying sweeps is maximal 3800 ms. Please record the sweeps in MC_Rack, but export the data with MC_DataTool to custom ASCII import programs, for example to Matlab, for further analysis.

After recording long sweeps with "Window Extent" settings near to 3800 ms, and replaying the respective *.mcd file with the MC_Rack Replayer, please slow down the "Replay Speed" in the "Replayer" tab. Otherwise MC_Rack might have problems with displaying the data.

3.3.2 Monitoring Triggered Activity

Next, you need a Data Display for monitoring the ongoing activity.

Step by Step Tutorial

Click in series with the Trigger Detector to the virtual rack. (If you would put both instruments in parallel, you would not be able to use the trigger stream generated by the Trigger Detector for triggering the Data Display, because virtual instruments can only use the output streams of other virtual instruments that are upstream in the virtual rack tree.)

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). When you have changed the channel map, the last used channel map is loaded automatically as the default.

on the toolbar or click Add Data Display on the Edit menu to add a Data Display

1. Define the display layout and select the data stream as explained before.

Triggering the display

To graph the sweeps synchronized to the stimulation, you need to start the display on the trigger event generated by the Trigger Detector that we set up earlier.

1. In the tree view pane of the virtual rack, select the Display 1, and click the Window tab.

2. Select the option Start on Trigger. In the Trigger selection box, Trigger 1 appears automatically. It is the only trigger data stream available in this rack. (You could set up multiple Trigger Detectors and trigger multiple displays on separate trigger events.)

Starting MC_Rack

 Click Start

(either on the Measurement menu, the toolbar, or the Rack tabbed page) to

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.

3.3.3 Recording Triggered Data

In principle, you could record the evoked responses continuously, and trigger the displays and analyzers when you replay the data. However, you would produce a huge amount of useless data, as generally only the response following the stimulus is of interest. Therefore, it is recommended to produce triggered data, that is, to cut out sweeps around the trigger event. This saves a lot of disk space.

Selecting data streams and channels for recording

Select the Recorder in the virtual rack tree view pane and then click the Channels tabbed page. On the white pane on the left of the Channels page, you see the data streams that are available with your data source settings, for example, the Analog Raw Data, Digital Data, Electrode Raw Data, and Trigger streams. (It does not matter whether you have really connected a device to the inputs, though.)

Click the data stream that you are interested in, that is generally the Electrode Raw Data stream, and the Trigger stream. The available electrode channels appear in a button array on the right side.

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. Confirm by clicking Save.

The file extension for the data files is *.mcd.

File size limit

When the maximum file size specified by the user has been reached, a new file is generated automatically. The file name is extended by four digits, counting up, for example LTP-Parameters0001.mcd, LTP-Parameters0002.mcd, and so on.

If you rather prefer that the recording is completely stopped when a file has reached the maximum size, please select the option Auto Stop.

For information on more options, please see "Generating Data Files" in the MC_Rack Features section.

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. In the Trigger selection box, Trigger 1 appears automatically. Two text boxes appear, too. These two parameters define the cutout: The Start Time is generally a negative value, that is, the pretrigger time. The Window Extent is the total time of the cutout sweep. Please read chapter "Triggering MC_Rack on a stimulus" for more information about "Window Extent" settings.

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. Please read the MEA2100-System manual for detailed information. At the moment five types of headstages are available for the MEA2100-System, which can be connected to the interface board once or twice: A headstage for one MEA with 32 (MEA2100-HS32), 60 (MEA2100-HS60) or 120 electrodes (MEA2100-HS120), and headstage for two MEAs with 32 (MEA2100-HS2x32) or 60 electrodes each (MEA2100-HS2x60). One or two headstages can be connected to the interface board (IFB) of the MEA2100-System.

MEA2100-32-System

Step by Step Tutorial

The MEA2100-32-System is a system providing all functions of a MEA2100-System, with the exception of the real-time feedback via DSP. In “Data Source Setup” it is present as an own device “MEA2100-32”. Please read the MEA2100-System manual for detailed information.

Using MC_Rack Software

Data Source Setup

Every MEA of the system can be operated completely independently by one instance of MC_Rack. To be able to open more than one instance of MC_Rack, please first open the "Advanced Configuration" dialog in the "Edit" menu.

Please increase the maximum number of instances according to the number of MEAs you are going to use in parallel:

 one MC_Rack instance for one HS32, HS60 or one HS120,

 two MC_Rack instances for one HS2x32, HS2x60, or for two HS32, HS60 or two HS120,

 four MC_Rack instances for two HS2x32 or HS2x60.

Afterwards you can open several instances of MC_Rack and assign every instance to one MEA of the system.

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.

If a MEA2100-HS2x60 is connected you have additionally to select the "Block" in the right drop down menu of “Virtual Device Configuration”. For the first instance of MC_Rack, select Block 1 (Channel 1…64) and for the second instance Block 2 (Channel 65…128). Select the appropriate MEA type from the drop down menu for each instance. If a second headstage is connected to the same interface board, it will become available in the "Data Source Setup" as MEA2100 (S/N: XXXXX-B). The settings for the second headstage are analog to the first.

Hardware Settings for the MEA2100-System in the Data Source

When using the MEA2100-System, the “Hardware” tab of the MC_Rack software is modified. Please see also chapter “Defining a Data Source”.

In the "Hardware" tab of the Data Source, the gain setting must be adjusted to ensure a correct scaling of the data in MC_Rack. The gain is a fixed hardware property, while sampling frequency and input voltage range of the data acquisition board can be selected according to the demands of the experiment.

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. It is advisable to select the input voltage range as small as possible, to ensure an optimal A/D resolution of the analog input signals.

The “Sampling Frequency” should also be selected as low as possible, depending on the signals you like to measure, to minimize data file size.

If several instances of MC_Rack are used to operate the MEA2100-System, for example with a MEA2100-HS2x60 headstage or two MEA2100-HS120 headstages, each instance of MC_Rack operates independently; you can define the “Input Voltage Range of Data Acquisition Board” and the “Sampling Frequency” for each instance of MC_Rack individually.

Hardware Filter Settings

While the MEA2100-System in principle can measure DC signals, this is for most purposes very impractical, as the baseline would constantly drift. Therefore the system is equipped with software configured hardware filters. By default, a second order high pass filter with a cut off frequency of 1 Hz is used to prevent a baseline drift. The upper cut off frequency is 3.3 kHz. Additionally you can use the software filters of MC_Rack, if necessary.

Note: It is possible to change the settings of these filters without modification of firmware or hardware via the add on program ”MEA2100 Configuration”.

Setting up the Internal Stimulus Generator of the MEA2100-System

The headstage of the MEA2100-System is equipped with an integrated 3-channel stimulus generator. The three stimulation channels operate independently. If two instances of MC_Rack are used to operate one headstage, each MC_Rack instance works completely independent, so three stimulation channels are available for each instance. If four instances of MC_Rack are used to operate two headstages, for example MEA2100-HS2x60, each MC_Rack instance works independent respectively, so twelve stimulation channels are available, three for each instance.

It is possible to choose between current or voltage controlled stimulation, and any electrode can be selected for stimulation. The control functions for electrode selection and definition of the stimulation parameters are integrated into MC_Rack, you do not need any additional software. However, it is possible to import stimulation patterns generated in MC_Stimulus II as ASCII data.

Add the internal stimulus generator to your rack: Click menu “Edit” and choose "Add MEA2100 Stimulator".

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.

The individual stimulation pulse is defined in the "Pulse" window. Set up a monophasic pulse by selecting the voltage / current in mV/μA and the duration time T1 in μs. For setting up a biphasic pulse you have to select the stimulation strength and time also for the second phase. The shape of the pulse is displayed immediately in the window below. Once started, a programmed paradigm will run to its’ end, or till it is manually terminated.

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.

When using the "Train" window for setting up a pulse train, please select the "Inter Pulse Interval IPI" in μs and the number of pulses in the train in "Repeat". If no pulse train is needed, set the IPI to zero and the Repeat to one.

The "Inter Train Interval ITI" function can be used to repeat a single pulse or a pulse train.

The interval time can be set in ms, and also the number of repeats. The complete programmed paradigm is shown in the graphical display below the stimulus window.

Once started, a programmed paradigm will run to its’ end, or till it is manually terminated.

If the “Continuous Mode” is activated, the paradigm will be repeated indefinitely, till manually stopped. Please note that stimulation does not stop when MC_Rack is stopped.

Importing a stimulation file created with MC_Stimulus II

To generate more complex stimulation patterns it is possible to import a stimulation file setup with the MC_Stimulus II software as ASCII data. Please read the respective stimulus generator STG manual for detailed information about creating a stimulus file. You can import any pulse type available in MC_Stimulus II.

 Program the file in MC_Stimulus II as usual; channel 1 will become stimulus 1 in MC_Rack,

channel 2 will become stimulus 2, and channel 3 will become stimulus 3.

 Export the file as ASCII file (MC_Stimulus II: File - Export ASCII)

 Import this file in MC_Rack (Stimulus Tab: Import File)

It is not necessary to program Sync Out pulses. Information in MC_Stimulus Channel 4 and up all Sync Out channels will be ignored.

The “Stimulus” interface will be disabled and the imported pattern will be shown in the graphical stimulus display. To skip the imported pattern and reactivate the “Stimulus” interface, click the “Unload File” button.

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.

Important: MC_Rack must not be running in "Play or Record" mode to be able to start a stimulation paradigm, but a running paradigm will continue even after MC_Rack is stopped. Once started, a programmed paradigm will run to its’ end, or till it is manually terminated.

If "Manual" is selected in the "Trigger" drop down menu, the "Start" and "Stop" buttons can be used to control the stimulation manually.

If "Start" is selected, the stimulation starts as soon as MC_Rack is started (in "Play" or "Record" mode). A delay between start of MC_Rack and start of stimulation in ms can be selected in the "Pre" time window. You can stop the stimulation paradigm by pressing the "Stop" button.

If a "DigIn" is selected, the stimulation starts if a TTL pulse is delivered to the respective connectors Digital In 1 to 4 on the front of the MEA2100-System interface board.

If the internal STG is connected to one or more "Trigger Detectors" in the MC_Rack virtual tree, it is also possible to start the stimulation on any of these Triggers (Trigger 1, 2 …).

If the “Real-time Feedback” tool is activated, any of the internal STG can be started on one of the conditions defined in the Real-time Feedback tool (RF1, RF2, …). Please see chapter “Real-time Feedback with MEA2100-System” for more information. The tool must be present and active, for the Real-time Feedback conditions to become available.

If a new trigger arrives before the programmed stimulation paradigm is finished, the paradigm starts again from the beginning. All three stimulus channels can be started and stopped independently.

To repeat a stimulation pulse in a loop, activate the “Continuous Mode”. The pulse will be applied continuously until it is stopped by manually with the “Stop” button.

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. To apply the stimulation pattern to all electrodes, click the button “All” below the grid. Electrodes can be grounded or selected as regular recording electrodes (Not Stim.) in the same way.

Electrodes selected for stimulation pattern 1 “Stim.1” are colored in blue, for stimulation pattern 2 “Stim. 2” are colored in red, or stimulation pattern 3 “Stim. 3" are colored in yellow. To cancel a stimulation electrode, please use the radio button “Not Stim.” and click on the selected electrode.

Blanking

The blanking feature to avoid stimulation artifacts can be activated or deactivated via the check box “Blanking”.

A blanking signal transiently switches off the input stage of the amplifier during the stimulus, thus avoiding stimulus artifacts on non-stimulating electrodes.

Amplifier saturation is effectively prevented and the recovery time is greatly reduced. During the blanking period, a flat line is displayed. This blanking period extends a few hundred microseconds before and after the actual stimulus, currently 600 μs, but might be subject to change. The preand post-time are experimentally optimized and can not be changed by the user.

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. This sometimes causes switching artifacts independently from the actual stimulation.

However, if the function “Dedicated Stimulation Electrodes” is active, the selected stimulation electrodes will be constantly connected to the stimulator outputs. This causes permanent higher noise on the selected stimulation electrodes, and makes of course recording on the stimulation electrodes impossible, but almost completely removes residual artifacts. The images below show stimulation on electrode F3 with and without “Dedicated Stimulation Electrodes” activated.

Note: The artifact suppression additional to blanking via “Dedicated Stimulation Electrodes” is not available when using the “List Mode”.

“Dedicated Stimulation Electrodes” selected (X-Axis: 1000 ms, Y-Axis: +/- 500 μV)

“Dedicated Stimulation Electrodes” deselected (X-Axis: 1000 ms, Y-Axis: +/- 500 μV)

List Mode

Clicking the button List Mode opens an additional window: List of Stimulation Patterns. In List Mode it is possible to generate and download a list of up to 256 user defined stimulation

patterns, which will then be applied automatically one after the other.

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. The step from one stimulation pattern to the next in the list happens when the start condition defined for Stimulus 1 occurs (for example, manual start, incoming trigger, real-time feedback trigger) and all three stimulator units are idle. Please see the red bars on the picture. However, the next pattern can only be started by the respective starting condition when the previous stimulation paradigm, including all breaks, is completely finished.

That means, if one stimulation pattern of any of the three stimulator units is still running when the condition occurs, nothing will happen. This also holds true when a stimulator unit is not actually used in the currently active stimulation pattern.

Hence, the longest programmed stimulation pattern determines the minimum possible time between two starting triggers, even if the respective stimulator unit is not actually used. It is therefore advisable to set a stimulation pattern with a length of 0 on all unused stimulator units, and keep all patterns as short as possible.

A stimulation pattern can contain single or multiple stimulation electrodes and may get an user defined name. To create a list of different stimulation patterns, please do the following.

Click the button “List Mode”. There are two windows in the “List of Stimulus Pattern”. The small window on the right side is for typing in a name for a pattern. In the window on the left side the list of stimulation pattern will be displayed and arranged.

When opening the “List Mode” for the first time, the term “New” appears and the current stimulation pattern is the first stimulation pattern in the list. To change the name, please overwrite the name with the specific name of this pattern in the small window.

To insert a stimulation pattern, select with the mouse the position in the list where you want to place the pattern. The line will be highlighted in blue. Type the specific name of this pattern in the small window. Click the button "New" and the new list entry appears.

To append a pattern, select the line under the last list entry. The line will be highlighted in blue. Type the specific name of this pattern in the small window. Click the button "New" and the new list entry appears.

To rename a pattern of the list, select the pattern which will be highlighted in blue. Then you can change the name of the pattern in the list. Please click the “Rename” button.

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. The trigger start in Stimulus 2 and Stimulus 3 tab will not be available, but all three triggers run simultaneously.

The stimulation patterns from the list will be applied one after the other and change every time the start condition defined for Stimulus 1 occurs and all three stimulator units are idle, as described above. When the end of the list is reached, the software jumps back to the first pattern and continues. When the “Restart” button is pressed, the software jumps to the first entry in the list, respectively.

Use of the Digital Channel in the MEA2100

In contrast to the other MEA- and ME-Systems from Multi Channel Systems, the 16 input bits of the digital channel are not all accessible for external trigger signals, but are mostly used for internal communication between the different components of the MEA2100 system. Only the first four bits are connected to the physical DigIn connectors on the front side of the MEA2100 interface board. Most bits are permanently assigned to certain functions. However, these settings can be customized if necessary. Please see the channels assignments from the following table.

Bit 0 DigIn 1 Digital In channel 1

Bit 1 DigIn 2 Digital In channel 1

Bit 2 DigIn 3 Digital In channel 1

Bit 3 DigIn 4 Digital In channel 1

Bit 4 Stimulus 1 Stimulation pattern on channel 1

Bit 5 Stimulus 2 Stimulation pattern on channel 2

Bit 6 Stimulus 3 Stimulation pattern on channel 3

Bit 7 Zero not connected

Bit 8 RF 1 Real-time feedback specification 1

Bit 9 RF 2 Real-time feedback specification 2

Bit 10 RF 3 Real-time feedback specification 3

Bit 11 RF 4 Real-time feedback specification 4

Bit 12 RF 5 Real-time feedback specification 5

Bit 13 RF 6 Real-time feedback specification 6

Bit 14 RF 7 Real-time feedback specification 7

Bit 15 RF 8 Real-time feedback specification 8

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. The stimulation channels are connected to the last three bits, bit 13 to stimulus 1, bit 14 to stimulus 2 and bit 15 to stimulus 3. The channels are labeled according to their function in the digital display.

To record the digital data stream in the data file, please enable the respective check box in the “Channels" tab of the Recorder tool.

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. So to trigger, for example on each pulse of Stimulus 1, a Trigger detector in MC_Rack must be set to the Digital Channel, bit 4. Please see screenshot below.

It is also possible to set the trigger detector to react on a signal from any of the three STG units. This might for example be useful to start a triggered recording if a stimulus is applied from any of the STG units. All three bits must be unmasked, and the bit value must be defined as > 0. See chapter “Triggering on TTL Pulses” for more information.

Triggered recording and any instrument which is below the Trigger Detector in the virtual tree of MC_Rack can now work in relation to the selected STG unit(s).

Real-time Feedback with MEA2100-System

Important: The Real-time Feedback function is not available for the MEA2100-32-System!

The interface board of the MEA2100-System is equipped with a high-capacity digital signal processor DSP. By moving the detection and analysis of signals from the data acquisition computer to the digital signal processor inside the interface, it is possible to run online filtering, analysis and feedback stimulation in real-time. Please read also chapter “Real-time Feedback”.

At the moment, the real-time feedback is available for one instance of MC_Rack, that means for one MEA2100-HS60, one MEA2100-HS120, or one MEA of a MEA2100-HS2x60.

By default, eight of the 16 bits of the digital channels are permanently assigned to the Real-time Feedback function. For each of these eight bits, a different condition can be defined to release a trigger signal. These eight bits can be monitored with the Digital Display. See also “Use of the Digital Channel in the MEA2100”. The Real-time Feedback trigger signals are available in the “Trigger Detector”, and can also be directly selected to start the internal stimulus generators. See also chapter “Starting and Stopping the Stimulation”.

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

However, the dialog of the “Feedback Logic” tab is different for MEA2100-Systems. While the user can freely assign up o 16 different detection conditions to the 16 bits of the Digital Out channel in the other MEA- and ME-Systems, the MEA2100 offers by default up to eight conditions permanently assigned to eight bits of the Digital Channel. See also “Use of the Digital Channel in the MEA2100”.

in the toolbar. Please also read the chapter “Real-time Feedback” for details.

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. The headstages come preconfigured with different frequency bands by Multi Channel Systems MCS GmbH, and are labeled with A, B, C and D. The “Scan” function searches the complete frequency band and will detect all active headstages in range, and the radio buttons of the available headstages will become enabled in the “Select headstage” window. Now you can select one of the headstages for experimental processing only, the headstages do not work in parallel. In this example W8 headstages are connected and “A” is selected. Individual recording channels can be activated (pressed in) or deactivated. Inactivating channels can increase battery lifetime of the headstage.

Note: Deactivated channels will vanish from displays and will be automatically deselected in analysis instruments (Analyzer, Spike Analyzer or the like). When reactivated, channels automatically reappear in displays, but must be manually reselected in the “Channels” tab of analysis instruments.

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. Switching off the LED will save a little bit of energy. Select “Blink” and the LED flashes during recording. Select “On” and the LED will be on permanently. This feature can be used, for example for camera tracking. The W32-headstage is equipped with two LEDs, a blue one and an additional red one which can be switched independently of each other. The user has the same options to set the red LED. Both LEDs together improve the camera tracking, because with two LEDs it is possible to track the orientation of the headstage.

Choose a “RF Output Power” value from the drop down menu. The smaller the value, for example –18 DB, the longer the storage battery will support the recording, but the smaller the distance between animal and receiver.

When operating a wireless in vivo system, there is an additional “WPA” status display for visualizing the current status of the connected headstage in the status bar at the bottom of the MC_Rack window.

The WPA status display appears in green color when the W8-System is running. The color turns

into yellow

three seconds after the data acquisition is stopped. The yellow color indicates a stand by mode: The headstage is in energy saving mode, but can be started again by pressing the MC_Rack “Start” button.

The WPA status turns red if the recording system does not have contact with the selected headstage. This can be the case if the “Switch off” button has been used to send the headstage into “Switched Off” mode, if the battery of the headstage is removed, or if the headstage is out of transmitting range.

The status will automatically become green or yellow again if a headstage comes back into range.

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. Data Source Setup is only available as long as your current virtual rack is empty (that is, only a Recorder, but no MC_Card / USB based data acquisition or Replayer in the virtual rack). Configure the channel layout first

and then set up the rack configuration, because it is not possible to change the data source setup or channel layout later.

The data source and channel layout configuration is saved together with the rack (*.rck) file, that is you can set up different racks for different hardware configurations. For example, the number of electrode channels may vary in different ME-System setups. As a MEA-System user, you only have to decide whether you have a MEA60-System (with a 64 channel MC_Card) or a MEA120System (with a 128 channel MC_Card) or a USB based data acquisition. The number of electrode channels is fixed and cannot be changed for a MEA-System, but it can be altered in USB based data acquisition systems.

You can also select Simulation as the data source. In Simulation mode, no data is acquired from the MC_Card, but simulated waveforms are played and can be used for trying out MC_Rack features. You can choose between sine waveforms on all channels, or the default simulation (different waveforms on a number of channels). If no MC_Card is installed (or if it is not properly installed), only Simulation is available as the data source.

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.

Note: If you open a rack with a different channel layout, the channel layout of the opened rack will be used. You can check the data source setup of the loaded rack by selecting the data source in the tree view pane of the virtual rack, and clicking the Info tab, as shown in the following screen shot.

Important: Please note that the data source layout you choose (1-dimensional or 2-dimensional) does not only affect the numbering of the electrodes, but may also affect the compatibility with third party programs, for example, the MEA Tools. Make sure you always select the appropriate layout before setting up a virtual rack, and make always sure that the data source layout of the loaded rack file is appropriate before starting the data acquisition.

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. For the electrode channels, the original signal is calculated automatically according to the gain settings in MC_Rack. Signals on the analog channels are recorded "as is", with no respect to the gain.

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. To configure the MEA layout, please use the right drop down menu "MEA". To configure the amplifier, please use the left drop down menu "Amp" (MEA1060 without blanking circuit, gain factor 1200, and MEA1060BC with blanking circuit, gain factor 1100 for MEA-Systems, and FA64I/S, FA32I/S for ME-Systems).

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. The data source layout is 1 dimensional, with 16 electrode channels, and an additional digital channel.

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. The data source layout is 1 dimensional, with 32 electrode channels, and an additional digital channel.

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. The USB MEA device will be specified on the right Data Source drop down menu: USB-ME256 (S/N: 0004). The number in brackets is the serial number of the device. Adjust the number of channels available.

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

Note: Setting up the configuration of the data source is important for having the correct layouts for MEA A, B, C and D during the complete experiment.

USB-ME128 Data Acquisition

The USB-ME128 device is in principle the same device as the USB-ME256, except for the total number of channels, that is 128.

The USB-ME128-System does not require a MC_Card, but uses an USB 2.0 port for the data transfer to the data acquisition computer. Please see USB-ME128 manual for detailed information. Select USB MEA from the Data Source drop down list. The USB MEA device will be specified on the right Data Source drop down menu: USB-ME128 (S/N: 0002), for example. The number in brackets is the serial number of the device.

Note: Setting up the configuration of the data source is important for having the correct layouts for MEA A and B during the complete experiment.

USB-ME64 Data Acquisition

The USB-ME64 device is in principle the same device as the USB-ME256, except for the total number of channels, that is 64.

The USB-ME64-System does not require a MC_Card, but uses an USB 2.0 port for the data transfer to the data acquisition computer. Please see USB-ME64 manual for detailed information. Select USB MEA from the Data Source drop down list. The USB MEA device will be specified on the right Data Source drop down menu: USB-ME64 (S/N: 0002), for example. The number in brackets is the serial number of the device.

In USB-ME64-System it is possible to configure the MEA1060 / MEA1060BC amplifier. Additionally it is possible to configure the layout of MEA A.

Note: Setting up the configuration of the data source is important for having the correct layout for MEA A during the complete experiment.

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). The number in brackets is the serial number of the device.

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. The W8-System device for example, will be specified on the right Data Source drop down menu: MCS WPA8 (S/N: 00001). The number in brackets is the serial number of the system. The data source layout is 1 dimensional, with 8 electrode channels and an additional digital channel.

Note: With all electrode channels, the maximum sampling rate for the Wireless Recording System is 20 kHz. It is possible to increase the maximum sampling rate up to 40 kHz by deactivating at least four electrode channels. Please pay attention to the sampling rate respectively, when using the W4-, W16- or W32-System.

MC_Rack Features

MEA2100-System

Select USB MEA from the left Data Source drop down list. The MEA2100 device will be specified on the right Data Source drop down menu: MEA2100 (S/N: 0000-A).The number in brackets is the serial number of the system, the character A labels the connected headstage, A is the first headstage, B is the second headstage. It is possible to run up to two instances of MC_Rack per headstage . Please read chapter "Advanced Configuration". Specify the “Number of Channels” first: 32 electrode channels, when connecting one headstage with 32 recording and 12 stimulation electrodes (MEA2100-HS32), 64 when connecting one headstage with 60 channels (MEA2100HS60) or 128 electrode channels when connecting two headstages with 60 channels (MEA2100HS60) or one headstage with 120 channels (MEA2100-HS2x60 or MEA2100-HS120) to the interface board. Choose “Configuration” in the data source layout. Enable the check box for the digital input channels. Select the correct headstage in the “Amplifier” drop down menu and specify the type of MEA.

MC_Rack Manual

MEA2100-32-System

The MEA2100-32-System is a descendant of the MEA2100-System with the same functions except of the real-time feedback. Please read the MEA2100 Manual for detailed information. Select USB from the left Data Source drop down list. The MEA2100-32 or MEA2100-2x32 device will be specified on the right Data Source drop down menu: MEA2100-32 (S/N: 00018-A). The number in brackets is the serial number of the device. The data source layout is Configuration, with 32 electrode channels, and an additional digital channel.

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. If the settings are not appropriate, remove the MC_Card from your rack and change the channel configuration.

 Click the Hardware tab to define the other settings, like the amplifier gain and sampling

frequency.

Signal voltage range

Please define first the "Amplifier Gain" and then the "Input Voltage Range of the Data Acquisition Board". The "Signal Voltage Range" is calculated by dividing the "Input Voltage Range of the Data Acquisition Board" and the amplifier gain factor.

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. The original signal is calculated automatically from the input and the amplifier gain.

Important: The gain is a hardware property. You cannot change the gain of the amplifier with MC_Rack. Make sure you use the gain that the amplifier actually has. This is especially important if you use a PGA amplifier with programmable gain. Use the PGA-Control program to change the PGA's gain and make sure you specify the same gain in the MC_Rack program as well. Otherwise, the recorded data will have wrong voltage values.

 Click Enter... to change the amplifier gain settings.

Input voltage range of data acquisition board

You can adjust the input voltage range of the MC_Card from +/- 400 mV to +/- 4 V with the software control in the MC_Rack program. The lower the input voltage range, the higher is the voltage resolution. You need a higher input voltage range if your biological sample generates higher voltages, for example, cardiac signals from whole-heart preparations, and / or if the amplifier gain is higher, so that the amplified output signal amplitude is higher, too. For spike data, an input range of -819 to +819 mV will in most cases be fine, whereas for sum field potentials like LTP that can be in the range of mV, you will probably need a higher input range.

For example, if you have a standard MEA amplifier with a gain of 1200, and choose a MC_Card input voltage range of 819 to +819 mV, this results in a signal input range of -682 to +682 μV.

With a MC_Card with 14-bit resolution and an input voltage range of -819 to +819 mV, the voltage resolution of the MC_Card will be 0.1 mV or 100 μV: A 14 bit resolution means 2

= 16384 available voltage values. 819 mV * 2 = 1638 mV total input voltage range / 16384 = 0.1 mV. For a standard MEA amplifier with a gain of 1200, this means a resolution of 83 nV for the recorded original signal.

 Select the desired input voltage range from the Input Voltage Range of Data Acquisition

Board list.

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. The maximum sampling rate is 50 kHz.

Please note that the sampling rate influences the amount of disk space needed and the computer performance. Do not use a higher sampling rate than necessary. If you have a low signal frequency (for example, from heart cells), you can use a much lower sampling rate than if you have high frequency signals (for example, from neurons). (For more information on recording and file size see "Recording Data").

If the sampling rate is too low, you will miss signals and / or see artifacts. The sampling rate should also be at least twice the bandwidth of the MEA1060 amplifier. Otherwise, aliasing occurs. See also the chapter "Filtering and Sampling Rate" for more information about aliasing.

Note: The sampling frequency should be at least five times the highest signal frequency and at least twice the bandwidth of the MEA1060 amplifier.

 Select the desired sampling frequency from the Sampling Frequency list.

Maximal Sampling Frequency using the data acquisition devices USB-ME256 and USB-ME128

Usually, the maximal sampling frequency for MCS data acquisition systems is 50 kHz. However, when using some advanced features of the USB-ME256 and USB-ME128, some limitations apply.

The maximal sampling frequency that can be achieved with 256 channels is 40 kHz. This is possible when using the USB-ME256 with the "virtual device configuration" 1 x 256 (Please see Advanced Configuration). With the USB-ME256 and USB-ME128 it is also possible to split the data stream into 2 x 64 or 2 x 128 and into 4 x 64 channels, respectively, again by using the "virtual device configuration". These virtual machines can then be controlled independently by up to four instances of MC_Rack. However, splitting the data stream into several virtual devices consumes system performance. Therefore, the maximal sampling frequency is limited to 25 kHz when using the virtual device configuration 2 x 64 (USB-ME128) or 2 x 128 and 4 x 64 channels (USB-ME256).

Offset Correction

An offset correction is generally not necessary, because the intrinsic DC offsets of the MCS amplifier outputs and the MC_Card are very low in comparison to the signals of interest. You can use the offset correction feature to remove even this low offset and reset all channels to zero.

Note: If you observe a large offset on any channel(s), you should contact your local retailer for troubleshooting. The offset correction is not intended for removing large offsets, because the offset correction will decrease the input voltage range.

1. Click Offset Correction to activate the offset correction..

2. Click Learn Offsets to perform an individual offset correction for each input channel. MC_Rack takes 100 ms of the recorded data in the moment when the button is pressed to calculate the DC offset. The mean of this 100 ms sweep is subtracted from the recorded data as long as the Offset Correction button is pressed. The individual offset values for each channel are saved in the local settings of the data acquisition computer and are only overwritten when you click Learn Offsets again. Make sure you press the Learn Offsets button only when you have no real input signals or irregular noise signals on the electrodes. To be on the safe side, you can connect a test model probe to the amplifier.

MC_Rack Manual

4.2.3 Channel Tool

Click the "Channel Tool" icon from the Edit menu. The following dialog appears. Click the "Channels" tab.

in the main window toolbar, or select "Channel Tool"

Select the data stream you want to apply the channel tool: Electrode Raw Data in this example. Select a "Reference electrode" from the "Reference electrode" drop down menu.

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. Add the MC_Card to your rack, and click the Group tabbed page to define the groups. This page is only available if you use a 1 dimensional channel layout (see Setting Up the Channel Layout).

2. Define the number of electrodes with multiple channels. On the right, the layout is updated accordingly. Each column represents a multitrode.

3. Define the number of channels per electrode. The number of rows is updated accordingly.

4. Assign the appropriate channel numbers to each channel.

You can load or set up predefined channel maps. See Setting Up a Channel Map for more details on the subject.

4.2.5 Simulation Mode

The simulation mode is available for users who are interested in learning more about the MC_Rack features, but do not have a MC_Card or an USB based data acquisition available. Without a properly installed MC_Card or other hardware, MC_Rack starts in Simulation mode automatically. However, you can also switch from the default mode to the Simulation mode if you have installed a MC_Card or an other device, for example, if you want to prove MC_Rack without connecting an amplifier.

In Simulation mode, no data is acquired from the MC_Card or from USB based data acquisition, but simulated waveforms are played and can be used for trying out MC_Rack features. You can choose between sine waveforms on all channels, or the default simulation (different waveforms on a number of channels). The third option is "File Source". Selecting this option an additional window pane appears and you are able to browse through your folders.

If no MC_Card is installed (or if it is not properly installed), only Simulation is available as the data source.

Warning: Make sure that you select the MC_Card starting an experiment. You cannot use a virtual rack that uses Simulation as the data source for experiments. With Simulation as the data source, no data will be acquired from the MC_Card.

as the data source (not the simulation) before

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".

With the option "File Source" in simulation mode you can open binary files with the extension ".raw" for simulating data. It is recommended to create these binary files with the software MC_DataTool, but you can use different software just as well, however the format of the file has to be binary.

Note: When creating a binary file with MC_DataTool, make sure to export as many channels to the binary file as should be simulated later.

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. Data streams are either acquired by the MC_Card or an USB based data acquisition device, for example, Electrode Raw Data, Analog Raw Data, and Digital Data; or they are generated by MC_Rack when processing input streams, for example, Trigger, Parameter, Spikes and Filtered Data.

You can adjust the number of analog and electrode channels according to your hardware in the Channel Layout dialog box, up to a total of 256 channels. One digital input stream with 16 channels (input bits) is available.

If you assign data to MC_Rack instruments, for example, the Recorder, you can select complete data stream(s), or you can pick individual channels of interest from a data stream.

In the following list, all data streams available in MC_Rack are briefly described. Some more complex data stream types are explained in more detail in the following chapters.

Definition of Data Stream Types

Electrode Raw Data:

Analog Raw Data:

Digital Data:

Unprocessed analog data acquired from an amplifier, for example, from a MEA amplifier for MEA electrodes or from a ME preamplifier like MPA8I. The amplifier gain can be specified in MC_Rack, so that the original signal is calculated automatically.

Analog non-amplified data that is directly delivered to the MC_Card via BNC connectors, for example, channels A1, A2, A3 in the typical MEA layout. In USB-MEA- or USB-ME-Systems four additional analog channels are available. The data are delivered to the internal data acquisition, and send to the data acquisition computer via USB High Speed. You can use it to record additional information from external devices, for example, the heart rate, and so on. You can connect the Sync Out of a STG (stimulus generator) to an analog input to synchronize stimulus application and recording.

The 16 digital input channels of the MC_Card can be used to record additional information from external devices as a 16-bit encoded number, or you can connect the Sync Out of a STG (stimulus generator) to a single input bit for synchronizing stimulation and recording. A digital IN /OUT connector is also available in USB-MEA- and USB-ME-Systems. The 16 digital input channels are represented as the Digital Data stream, that is, a stream of 16-bit values, each bit (0 to 15) representing one digital input. Standard TTL signals are accepted as input signals on the digital inputs. There are two possible logical states for each bit: 0 (low = 0 V) and 1 (high = 5 V). The digital input channels are sampled with the overall sampling rate selected in MC_Rack.

In the standard configuration, TTL signal sources can be connected to 3 BNC inputs (input bits 0, 1, 2). Alternatively, a 68-pin socket supporting all 16 input and output bits and a digital in / out extension with 16 BNC inputs and outputs can be ordered as accessories. Unused input bits, which have an undefined state, should be masked in the Trigger Detector.

For example, if the digital input bit 0 is set to high, the binary 16-bit value will be 0000000000000001, or 1 as a decimal number. If channel 2 is set to high, the value is (binary) 0000000000000010, or (decimal) 2, and so on. Any combination of logical states of input bits is represented by the 16-bit value.

For more details on the use of the Digital Data stream for triggering MC_Rack, please see the chapter Trigger Detector under MC_Rack Features. For more back

round information on digital data and binary code, please see the

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. You can also program an automatic time-based trigger. The manual trigger allows the user to generate a trigger event manually during data acquisition.

Filtered Data:

Spikes: Generated by a virtual Spike Sorter. Spikes can be detected by a threshold

Parameter: Generated by a virtual Analyzer. Several independent parameters can be

Averager: Generated by a virtual Averager. You can average sweeps to enhance the

Generated by a virtual Filter. You can use several filters with different cutoff frequencies in your rack, for example, to remove background noise from your signals or to separate spike activity from local field potentials.

or by their shape. Spike data streams can be overlaid or displayed as a Raster Plot, sorted into up to three categories, or analyzed (the spike rate, for example).

extracted from the same or separate input streams, for example, the peakto-peak amplitude, the spike rate, and so on.

signal to noise ratio. The averaged data can be saved and displayed. In addition to the averaged data stream, a trigger data stream is created (Avg Trigger). This trigger event is the time point of the last sweep. You need this trigger information to access the averaged data later. See also Averaged Data for more information.

4.3.2 Channel Selection

In the dialog box of the Recorder, Filter, Spike Detector and Analyzer tool, click the Channels tab to assign individual channels to the according virtual instrument.

You can conveniently select and deselect channels with the button array on the right side. You can choose single channels for recording, analyzing or displaying simply by clicking the appropriate buttons.

The button array is arranged either in the layout of the MEA or in a linear fashion depending on the currently selected stream and channel layout.

Selecting a data stream

The button array of the selected data stream is shown. The currently selected stream is highlighted in blue. If you want to switch to the button array of another stream, select that stream in the tree view to update the button array.

 Click the desired data stream listed on the left. A button for each channel of the selected data

stream is shown.

Selecting a channel

The buttons represent single channels and have a toggle function. Click a button to select or deselect a channel.

 Click a button to select a channel. A selected channel button appears pressed in.

 Click a selected channel again to deselect it.

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. Continuous data means that the data is recorded / processed by the virtual instruments as a continuous data stream without regard to a trigger event. Continuous data may still be synchronized to another system by starting the recording of the file on a trigger event. Triggered data means that only data sweeps around a specific trigger event are displayed, saved, analyzed, and so on. This has nothing to do with the data stream types included in the data file: All data streams can in principle be recorded either continuously or triggered, though it generally does not make much sense for all data stream types. For example, the recording of spike cutouts would be a typical application for a continuous recording (even though the spike data stream itself is not really continuous, it is treated as a continuous stream in MC_Rack), and the recording of evoked field potentials like LTP would be typical for a triggered recording (synchronized with the stimulation). Extracted parameters like the spike rate are a special kind of data stream, because these data streams include only single data points. Trigger settings in the Recorder do not apply to parameter streams.

A trigger event can be a biological signal crossing a threshold, or an external trigger event, like a TTL pulse. The trigger event is specified with the Trigger Detector.

The Recorder, the Data Display, the Analyzer, and the Averager can be triggered by a trigger event. You can define several triggers and assign them to separate virtual instruments. Use the Window tabbed page of a virtual instrument to assign a trigger to it (Settings to assign a trigger to the Averager, ROI for the Analyzer).

Note: MC_Rack stores the last two seconds of recorded data streams in a temporary virtual memory. Therefore, it is not possible to display streams with sweeps that are longer than 2 s in MC_Rack. You can record longer sweeps and export the data to other analysis programs, though.

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.

Assigning a trigger event to a virtual instrument

You can trigger a virtual instrument by any Trigger data stream. The trigger event is referred to as a time point of 0.

In the following example, the virtual instrument starts to process the data 30 ms before the trigger and stops after a total time of 200 ms (170 ms post-trigger time). This results in 200 ms sweeps. Please read chapter "Triggering MC_Rack on a stimulus" for more information about "Window Extent" settings.

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. If you assign averaged data to another instrument, the Analyzer or a display, for example, you should use the Avg Trigger to trigger this instrument.

Recording averaged data

Together with the averaged data stream, the Avg Trigger is saved in the data file. You need this trigger when you assign the Averaged Data stream to another instrument, for example for triggering a Data Display.

Note: If you want to record averaged data and triggered data in the same data file, please make sure that the Start Time and Window Extent of the Averager and the Recorder match. Otherwise, you will not be able to review the Averaged Data stream later.

Replaying (or graphing) averaged data

In the following, it is described how to review an already save averaged data stream with the Replayer. For more information on how to generate an averaged data stream (either online during data acquisition or offline with the Replayer), please see chapter "Averager", "Averaging Data Sweeps".

For replaying recorded Averaged Data streams, click rack. Do not use the Averager, which is only used for generating Averaged Data streams!

In the tree view pane of the virtual rack, select the Data Display (here: Display 1), and click the Data tabbed page. Select the Averaged Data stream (here: Averager 1). You can select the raw data stream as well, to overlay the averaged data with the raw data, for example.

to add a Data Display to the virtual

Multichannel Systems MC-Rack User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual