MC_Rack Sample Racks Read Me
The offline racks and the demo data are provided in the Tutorial folder on the installation volume. The demo data need to be copied to the correct file path. Please copy the complete MC_Rack Tutorial folder into the MC_Rack directory with the following path.
c:\Program Files\Multi Channel Systems\MC_Rack\
Otherwise the file paths of the data files are not valid and the program cannot find the files, resulting in an error message. This is no problem, however, but you will have to select the data files manually.
The intention of the offline racks is to show possible applications, and how to set up a rack. It is not possible to use offline racks for recording.
The online racks can be used as templates for your experiments instead of setting up new racks from scratch. You only have to adjust the parameters according to your needs.
Sample Racks - Overview
Offline
The provided sample racks show two typical MEA applications and demonstrate the power and features of the data acquisition and analysis program MC_Rack. These racks are replaying recorded data files, that is, you can use these racks without a connected MEA System.
For more information about the racks and how to set them up, please refer to the step-by-step tutorial in the MC_Rack Help.
Neurobiology
Acute Hippocampus slice: fEPSP analysis, recording of an i/o curve
Consider you have recorded from an acute hippocampal slice on a Multi-Electrode Array (MEA) with 64 channels and you like to analyze the input-output relationship of an electrical stimulation.
The biological sample was 300 µm thick (see picture) and stemmed from a 22 days old rat. The tissue has been stimulated with one of the substrate integrated electrodes (#65). A monopolar electrical stimulation with biphasic voltage pulses (duration of 100 µs per phase) with amplitudes from 500 to 3000 mV, in 250 mV steps, was applied. Individual voltage steps were repeated 5 times with a delay of 5 s, that is, 5 x 500 mV, then 5 x 750 mV, then 5 x 1000 mV, and so on. The SyncOut signal of the STG (stimulus generator) was used to trigger the recording sweeps, with a pre-trigger of 10 ms and a time window of 70 ms.
This example shows a recording with the new MEA amplifier with blanking circuit, featuring a superior stimulus artifact suppression. The SyncOut signal of the STG also triggered the MEA amplifier. The electrodes were transiently (for 500 µs: SyncOut pulse 300 µs long, Wait settings 200 µs) separated from the amplifier stage during stimulation. Thus, stimulus artifacts could be efficiently prevented on all recording channels.
(Data kindly provided by Dr. Frank Hofmann, University of Heidelberg, Germany)
- Rack file: Hippocampus_IOCurve_Demo.rck
- Data file: I-Ocurve_Demo.mcd
- Image file: Hippocampus_IOCurve.jpg
LTP-Demo rack — Theta burst induced Long Term Potentiation (LTP)
This example file was recorded from an acute hippocampal slice on a Multi-Electrode Array (MEA) with 64 channels with the aim to analyze long-term potentiation (LTP) following electrical stimulation.
The 300 µm thick acute hippocampus slice was prepared from a 21 days old rat. The slice was stimulated every 60 s with a single biphasic pulse (1.5 V amplitude, 100 µs per phase) by one of the embedded MEA-electrodes (No. 75).
LTP was induced by an LTP train with 100 pulses of same amplitude and duration as the test stimulus, and a frequency of 100 Hz. The SyncOut signal of the STG (stimulus generator) has been used to trigger the recording, with a pre-trigger of 30 ms and a time window of 100 ms. Data was recorded before and after the LTP induction; the LTP induction itself was not recorded.
As the data was acquired with a MEA1060-BC amplifier with blanking circuit, all MEA electrodes were disconnected from the amplifier shortly during stimulation, in this case for 540 µs (300 µs Sync Out pulse of the STG, plus intrinsic Wait of 40 µs, plus user-defined Wait of 200 µs). This efficiently prevented stimulus artifacts.
(Data kindly provided by Dr. Frank Hofmann, University of Heidelberg, Germany)
- Rack file: Neuro_LTP_Demo.rck
- Data file: LTP-Demo.mcd
- Image file: LTP_slice.jpg
Paired pulse facilitation (PPF) and Depression (PPD)
In Paired Pulse Faciliation (PPF) or Depression (PPD) experiments, the stimulus is followed by a second stimulus, typically 20-60 ms later. The amplitude of the sum potential of the neuronal response to the second stimulus is compared to that of the first one. It is higher in case of a paired pulse facilitation, or lower in case of a paired pulse depression. Some electrodes recorded PPF and others PPD in this demo data file. For example, you can see a PPF on electrode 53, and a PPD on electrode 66.
In MC_Rack, two (or more) regions of interest (ROI) can be defined, one triggered by the first stimulus, the other by the second stimulus, for example. The peak-to-peak amplitudes for both ROIs can be extracted automatically and online.
The example data file was recorded from a 300 µm thick acute hippocampus slice that was prepared from a 32 days old rat. The slice was stimulated with a single biphasic pulse (2 V amplitude, 100 µs per phase) by one of the embedded MEA-electrodes (No. 64). The second stimulus pulse was applied 20 ms following the first one. Recording was triggered by applying the SyncOut signal of the stimulus generator to one of the analog input channels (A1). Recorded sweeps are 200 ms, with a pre-trigger time of 30 ms, and a post-trigger time of 170 ms.
As the data was acquired with a MEA1060-BC amplifier with blanking circuit, all MEA electrodes were disconnected from the amplifier shortly during stimulation, in this case for 540 µs (300 µs Sync Out pulse of the STG, plus intrinsic Wait of 40 µs, plus user-defined Wait of 200 µs). This efficiently prevented stimulus artifacts.
(Data kindly provided by Dr. Frank Hofmann, University of Heidelberg, Germany)
- Rack file: Neuro_PPF_Demo.rck
- Data file: PPF_Data.mcd
- Image file: PPF_Image.jpg
OTC Spikes Demo rack — Organotypic co-culture with spontaneous spike activity
Consider an organotypic co-culture of the dendate gyrus (DG) and the entorhinal cortex (EC) taken from a PND 6 rat, cultured for seven days. Both subregions show an independent spontaneous spike activity. Total recording time has been 60 seconds.
(Data kindly provided by Dr. Frank Hofmann, University of Heidelberg, Germany)
- Rack file: Neuro_OTC_Spikes_Demo.rck
- Data file: Neuro_OTC_Spikes_Demo.mcd
- Image file: OTC Spikes Image.jpg
Acute slices from cerebellum
You can also study acute slices from the cerebellum with the MEA System, for example for drug screening. The demo data shows typical signals from the cerebellum. Four selected electrodes of interest are marked with a white circle in the slice picture. Any standard MEA, for example with a medium spatial resolution (200/30), can be used for recordings from acute slices.
The demo rack shows the raw data from all 60 electrodes, and extracts the spike rate from four selected electrodes of interest.
(Data kindly provided by Dr. Ulrich Egert, University of Freiburg, Germany)
- Rack file: Neuro_Cerebellum_Demo.rck
- Data file: Cerebellum_Demo.mcd
- Image file: Cerebellum.jpg
Neuronal cell culture, drug testing
Data was recorded from a neuronal cell culture with rat striatum cells. The example shows the application of NMDA. Two demo data files are provided: neurons_NMDA_control.mcd before drug application, neurons_NMDA_5µM after drug application. The Analyzer extracts the spike number in 100 ms bins: Under control conditions, over 60 % of these bins are empty, that is, without spike activity. This demonstrates the organization of the spontaneous spiking activity in bursts. After NMDA application, the spiking activity is more randomn, demonstrated by the fact that only 8 % of the bins are empty. The overall spiking activity measured in 2 s bins and displayed in spike numbers is increased, too, but the main difference is how the activity is organized. (Data kindly provided by W. Fleischer, University of Düsseldorf)
- Rack file: Neurons_DrugApplication_Demo.rck
- Data files: neurons_NMDA_control.mcd (before compound application), neurons_NMDA_5µM.mcd (after compound application)
Retina
Field potential electroretinogram
The electroretinogram (ERG) is an extracellular field potential generated by the cells in the retina. So-called microERGs can be recorded with the MEA System from retina explants, for example, from rat or chicken. (Data kindly provided by NMI Reutlingen, Germany)
- Rack file: Retina_MicroERG_Demo.rck
- Data file: Retina_ERG.mcd
Spiking activity
Spiking activity is visible in the ERG traces as well and can be easily extracted from the underlying field potential with the Spike Sorter in Slope mode.
Alternatively, the field potentials can be removed by a 300 Hz High Pass filter, and spikes can be detected by setting a threshold. This sample rack demonstrates both methods, and the spike sorting feature.
The raster plot highlights the regular spike pattern. (Data kindly provided by NMI Reutlingen, Germany)
- Rack file: Retina_Spikes_Demo.rck
- Data file: Retina.mcd
Cardiomyocytes
Excitation map (chicken embryonic cardiomyocytes)
The two-dimensional MEA layout is ideally suited for showing the waveform propagation and measuring the conduction velocity in a cardiomyocyte culture. The demo data shown here was recorded from chicken embryonic cardiomyocytes at a sampling rate of 10 kHz with a gain of 1200, and a bandwidth of 1 Hz to 3 kHz.
- Rack file: Cardiomyocytes_ExcitationMap_Demo.rck
- Data file: Cardiomyocytes_60Ch.mcd
Excitation map (HL1 cell line)
The demo data used here was recorded from a cardiomyocyte cell line from mouse that retains a differentiated cardiac myocyte phenotype: HL-1 from Dr. W. Claycomb. The demo data file Cardiomyocytes_HL1.mcd was recorded from HL-1 cells at a sampling rate of 10 kHz with a gain of 1000, and a bandwidth of 1 Hz to 3 kHz.
- Rack file: Cardiomyocytes_ExcitationMap_HL1.rck
- Data file: Cardiomyocytes_HL1.mcd
QT prolongation
The QT interval is an important parameter for drug testing. It can be extracted from the cardiac field potential recorded with the MEA System. The demo data shown here was recorded from chicken embryonic cardiomyocytes at a sampling rate of 10 kHz with a gain of 1200, and a bandwidth of 1 Hz to 3 kHz. The data was filtered with a digital 2 Hz high pass filter in MC_Rack.
- Rack file: Cardiomyocytes_QT-Analysis_Demo.rck
- Data file: Cardiomyocytes_QT.mcd
Recording from human embryonic stem cell derived cardiomyocytes (hESC-CM)
Cardiomyocytes from human embryonic stem cells develop a spontaneous beating pattern and can be used for basic research, for example, in the field of implantation medicine, or for drug screening, for example, for arrhythmogenic effects. hESC-CM present the most advanced model in cardiac in vitro physiology. Recorded extracellular field potentials resemble remarkably electrocardiogram signals. MEA recordings can be combined with other methods, for example, calcium imaging, optical recordings, patch clamp. This example data file shows the spontaneous activity of hESC-CM. (cell density: 10-15,000 cells per square mm, amplifier gain: 1200, voltage input range: -2000 mV to +2000 mV, sampling frequency 10 KHz, electrode diameter: 30 micrometer, electrode spacing: 200 micrometer) (Data kindly provided by Ofer Binah, Rappaport Institute, Haifa, Israel)
- Rack file: hESC-CM_NoStim_Demo.rck
- Data file: hESC-CM_NoStim.mcd
Pacing hESC-CM with electrical stimulation
hESC-CM are usually paced at the lowest rate and voltage as possible, for example, a culture beating with 1 Hz would be paced at 950 ms rate with a typical biphasic stimulus pulse of +/-2 mV and 2 ms for each phase. For this experiment, MEA 200/30 with additional 4 pairs of large stimulating electrodes were used. Following the stimulus artifact, you can see the fast activation spike and the slow repolarization waveform. (cell density: 10-15,000 cells per square mm, amplifier gain: 1200, voltage input range: -2000 mV to +2000 mV, sampling frequency 10 KHz, electrode diameter: 30 micrometer, electrode spacing: 200 micrometer) (Data kindly provided by Ofer Binah, Rappaport Institute, Haifa, Israel)
- Rack file: hESC-CM_Stim_Demo.rck
- Data file: hESC-CM_Stim.mcd
Recording from HL-1 cell line
The demo data used here was recorded from a cardiomyocyte cell line from mouse that retains a differentiated cardiac myocyte phenotype: HL-1 from Dr. W. Claycomb. The demo data file Cardiomyocytes_HL1.mcd was recorded from HL-1 cells at a sampling rate of 10 kHz with a gain of 1000, and a bandwidth of 1 Hz to 3 kHz.
The signal rate and RR interval are graphed.
- Rack file: Cardiomyocytes_HL1_Demo.rck
- Data file: Cardiomyocytes_HL1.mcd
Recording from chicken embryonic whole-heart
The demo data shown here was recorded from an E13 chicken embryonic whole-heart preparation at a sampling rate of 10 kHz with a gain of 1200, and a bandwidth of 1 Hz to 3 kHz. The signal rate and RR interval are graphed.
- Rack file: Cardio_WholeHeart_Chicken.rck
- Data file: Cardio_WholeHeart_Chicken.mcd
Online
Continous monitoring and recording: Display_Continuous.rck
This is a very basic sample rack that contains only a Data Display. You can use it for a first test of your MEA amplifier and noise level with the provided model test probe, for example. You will need a fully set up MEA System for using this rack.
Triggered recording: Display_Triggered.rck
This is a very basic sample rack for recording triggered sweeps, for example after stimulation. The selected trigger input is bit 0 of the digital MC_Card input.
Parameters:
- Recorder: Start time (pretrigger) -100 ms, window extent (sweep time) 300 ms
- Trigger Detector: Dead time 3 ms, digital input bit 0
Basic rack for MEA1060-BC amplifier: MEA1060-BC.rck
Basic rack for recording triggered sweeps with gain settings (1100) for a standard MEA1060-BC amplifier.
Basic rack for double MEA layout: MEA-120-System.rck
A basic rack with two raw data displays, one for each MEA.
Basic spike detection: SpikeDetection.rck
Demonstrates basic spike detection in Threshold mode. One display shows the raw data and the spike detection; the spike detection level can be adjusted for each channel separately.
Both analyzers available in MC_Rack are used in this rack for extracting the spike rate: The standard Analyzer operates based on discrete time intervals (bins or region of interest). Extracted parameters are graphed in the Parameter Display. The event-based Spike Analyzer was specifically designed for extracting statistical parameters such as the interspike interval (ISI) or the rate from Spike data streams generated by the Spike Sorter. Extracted parameters are graphed in the Spike Analyzer Display.
Parameters:
- Recorder: Spike cutouts and spike rate selected for recording
- Spike Sorter: Spike detection level for each channel
Spike detection - threshold and slope mode: SpikeDetectionModes.rck
This is a more advanced rack demonstrating both methods of spike detection in comparison: (a) Raw data is filtered by a high pass filter; spikes are detected by defining a threshold. (b) Spikes are detected by waveform (Slope mode) in unfiltered data.
Parameters:
- Spike Sorter (Threshold mode): Spike detection level for each channel
- Spike Sorter (Slope mode): Slope and amplitude for all channels
Visualizing activity with software LEDs: Neuro_Spikes_LED_Display.rck
Similar rack as SpikeDetection, but with an LED display. Analyzer extracts spike number in 10 ms bins. Spiking activity is indicated by lighting up of the corresponding electrode in the False Color "LED" display. Another display shows the spike cutouts.
Parameters:
- Spike Sorter (Threshold mode): Spike detection level for each channel
Slope analysis of local field potentials: Neuro_LFP_SlopeAnalysis.rck
This rack is based on the Triggered_Display rack. The slope of the sum potential is extracted from the region of interest (ROI), and then plotted vs. time. For example, for LTP experiments.
Parameters:
- Recorder: Start time (pretrigger) -100 ms, window extent (sweep time) 300 ms
- Trigger Detector: Dead time 3 ms, digital input bit 0
- Analyzer: ROI (after stimulus) 2-5 ms
Recording spikes and field potentials in parallel: Neuro_Spikes+FieldPotentials.rck
Rack for recording spikes and field potentials in parallel. A 300 Hz high pass filter removes separates field potentials from spikes, and vice versa. Spikes and spike rates are extracted from the high-pass filtered data; field potentials and peak-to-peak amplitudes are extracted from the low-pass filtered data. An additional display shows the unfiltered raw data.
Parameters:
- Spike Sorter (Threshold mode): Spike detection level for each channel
Digital filtering: Bandpassfilter.rck
A combination of two digital filters acts as a bandpass filter: The first filter is a 300 Hz high pass filter, the following is a 3 kHz low pass filter, resulting in a total bandwidth of 300 Hz to 3 kHz. The display monitors the filtered and the unprocessed raw data.
Parameters:
- Filters: Adjustment of the cutoff frequencies
LTP experiments: Neuro_LTP_analysis.rck
For recording and analyzing LTP experiments. The SyncOut signal of the STG (stimulus generator) will be used for triggering the recording, with a pre-trigger of 30 ms and a time window of 200 ms. Connect the SyncOut to the digital input bit 0 of the data acquisition computer.
The Raw Data Display monitors the raw data. One Analyzer extracts the minimum and maximum of the response in region of interest I (shortly after the stimulus pulse), the other Analyzer extracts the slope of ROI II (the linear part of the falling edge of the field potential). As an example, the parameters are extracted only from channels 41 and 42. Please select the channels where you expect the largest response. Minimum and maximum are plotted versus time in a common display; the slope is plotted vs. time in a separate display.
Parameters:
- Recorder: Start time (pretrigger) -30 ms, window extent (sweep time) 200 ms
- Recorder: Channels of interest, for recording to hard disk
- Analyzers and Parameter Displays: Channels of interest (41, 42) for extracting parameters, regions of interest
Paired pulse facilitation (PPF): Neuro_PPF.rck
In PPF experiments, the stimulus is followed by a second stimulus, typically 50-60 ms later. The amplitude of the sum potential of the neuronal response to the second stimuls is higher than to the first one. The SyncOut signal of the STG (stimulus generator) will be used for triggering the recording, with a pre-trigger of 30 ms and a time window of 200 ms. Connect the SyncOut to the digital input bit 0 of the data acquisition computer.
In MC_Rack, two regions of interest (ROI) can be defined, one triggered by the first stimulus, the other by the second stimulus. The peak-to-peak amplitudes for both ROIs are extracted automatically and online. For triggering the two Analyzers, you could either use one of the additional SyncOut channels of the STG 2000 series, or you can use the standard recording trigger as well (as in this example). In this case, the dead time of the Trigger Detector should be set to a higher value (for example, 1000 ms) to make sure that only the first trigger input (correlating to the fist stimulus pulse) is used for triggering, and the second is skipped.
Parameters:
- Recorder: Start time (pretrigger) -100 ms, window extent (sweep time) 200 ms
- Recorder: Channels of interest, for recording to hard disk
- Analyzers and Parameter Displays: Channels of interest for extracting parameters, regions of interest
Longterm experiments: SpikeRate_5minBins.rck
The MEA System and the flexible data stream management of MC_Rack is ideally suited for longterm experiments, for example 24 h monitoring of the spike rate, for days or even weeks.
As demonstrated with this sample rack, the spike rate can be extracted in, for example, bins of 5 minutes, that is, the spike rate is continuously extracted in 5 min intervals.
In this example, the spike cutouts, and the extracted spike rate is stored onto hard disk. To limit the file size, a new data file is generated each 4 hours.
Parameters:
- Recorder: Channels of interest, for recording to hard disk
- Analyzer: Width of the time bin: 5 min, parameter of interest: Rate
Cardio recording: Cardio_Averaging+ExcitationMap.rck
The MEA system can be used for in vitro studies of the electrical properties of cardiac myocytes and, for example, effects of drug candidates on field potential waveforms and kinetics. The two-dimensional MEA layout is ideally suited for showing the waveform propagation and measuring the conduction velocity in a cardiomyocyte culture. The field potential duration corresponds to the action potential duration, that is, the QT interval in an electrocardiogram. It is measured from minimum of the Na+ peak to the maximum/minimum of the IKr current peak.
If you study spontaneously active cultures, you can trigger the analysis based on the easily detectable sodium peak of any one channel, in this example, channel 51. Please select a channel that shows a very clear and regular waveform.
Based on this trigger, the Averager sums up the waveforms. The signal-to-noise ratio and signal quality improves significantly with each window that is summed up. For example, the IKr current peak (T wave) should be very clearly visible after 50 windows.
The Analyzer extracts the maximum corresponding to the IKr current peak (T wave) following the sodium peak.
Parameters:
- Recorder: Channels of interest, for recording to hard disk
- Analyzer and Parameter Display: Channels of interest for extracting parameters, region of interest
- Averager: Number of summed up windows (50)
Cardio recording: Cardio_SignalRate+RRInterval.rck
This template rack shows how cardiac signals can be automatically detected with the Spike Sorter. The signal rate and the RR interval as parameters that characterize the beating rhythm are monitored online during the experiment, and are saved together with the raw data. The export features of the event-based parameter displays allow a direct export of the extracted parameters in universal ASCII format, or as a graphics file.
In this configuration, the Spike Sorter operates in Threshold mode, that is, a signal is detected when the threshold is reached. The signal detection level can be adjusted for each recording electrode, according to the signal to noise ratio. The StdDev feature allows to automatically determine an appropriate threshold value for each channel in parallel, based on the standard deviation.
The Spike Analyzer extracts the signal rate and the interspike interval. Both parameters are plotted over time in the Spike Analyzer Display.
Parameters:
- Recorder: Channels of interest, for recording to hard disk
- Spike Analyzer: Channels of interest for extracting parameters, appropriate detection level for signal detection
- Spike Parameter Display: Channels of interest for extracting parameters, x and y axes ranges
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