Harvard Bioscience Multi Channel Systems Smart Ephys... User guide

CMOS-MEA5000-System
Manual

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Printed: 22.06.2021
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Table of Content
1 Important Safety Advice ..............................................................................................................5
1.1 Guarantee and Liability..............................................................................................................6
1.2 Operator's Obligations ..............................................................................................................6
2 Introduction...................................................................................................................................7
2.1 Welcome to the CMOS-MEA5000-System.................................................................................7
3 Hardware .......................................................................................................................................8
3.1 Headstage ................................................................................................................................8
3.2 Chip Orientation inside the Headstage………...…...……………………………………………….8
3.3CMOS-MEA Chip......................................................................................................................9
3.4IFB-C Multiboot Interface Board..............................................................................................12
4 Hardware Setup ..........................................................................................................................16
5 Installation of the Software.......................................................................................................17
5.1 System Requirements..............................................................................................................17
5.2 Testing the CMOS-MEA5000-System......................................................................................18
6General Software Features ........................................................................................................21
7CMOS-MEA-Control Software....................................................................................................23
7.1 Introduction ............................................................................................................................23
7.2 Main Window.........................................................................................................................23
7.3 Menu Bar................................................................................................................................24
7.4 Control Section.......................................................................................................................29
7.5 Data Display ............................................................................................................................33
7.5.1 Activity .........................................................................................................................33
7.5.2 Sensor Array Tool .........................................................................................................37
7.5.3 Spike Tool.....................................................................................................................43
7.5.4 Stimulation ...................................................................................................................46
7.5.5 Analog Channels ..........................................................................................................47
7.5.6 Digital Port Events.........................................................................................................47
7.5.7 Detailed View: Region of Interest..................................................................................48
7.5.8 Single Sensor View .......................................................................................................49
8 Operating CMOS-MEA-Control..................................................................................................50
8.1 Recording ...............................................................................................................................55
8.2 Stimulation .............................................................................................................................61
9 CMOS-MEA-Tools........................................................................................................................74
9.1 Main Window.........................................................................................................................74
9.1.1 Menu Bar .....................................................................................................................75
9.1.2 Tool Bar........................................................................................................................78
9.1.3 Analysis ........................................................................................................................80
9.2 Control Window .....................................................................................................................84
9.3 Data Display and Settings Window .........................................................................................89
9.3.1 Filter .............................................................................................................................89
9.3.2 Raw Data Explorer ........................................................................................................91
9.3.3 Spike Explorer Window.................................................................................................95
9.3.4 Network Activity: Network Explorer Window ................................................................99
10 Spike Sorter Tool.....................................................................................................................109
10.1 User Interface......................................................................................................................109
10.1.1 Processing View........................................................................................................109
10.1.2 Chip Overview ..........................................................................................................110
10.1.3 ROIs in Progress ........................................................................................................112
10.1.4 Log...........................................................................................................................112
10.1.5 Remote Sorting Clients .............................................................................................113

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10.2 Results View ........................................................................................................................113
10.2.1 Toolbar.....................................................................................................................113
10.2.2 Units List...................................................................................................................115
10.2.3 Filters and Sorting.....................................................................................................116
10.2.4 Chip Overview ..........................................................................................................117
10.2.5 Unit Comparison ......................................................................................................118
10.2.6 Unit Details...............................................................................................................119
10.3 Spike Sorter Settings ...........................................................................................................122
10.3.1 ROIs..........................................................................................................................122
10.3.2 Computing ...............................................................................................................123
10.3.3 Sorting .....................................................................................................................124
10.3.4 Peak Detection .........................................................................................................125
10.3.5 Post-Processing.........................................................................................................126
10.3.6 Presets......................................................................................................................127
10.4 Spike Sorting Client.............................................................................................................128
10.4.1 Spike Sorter Client on Linux......................................................................................129
10.5 File Format ..........................................................................................................................129
11 Tutorials ...................................................................................................................................131
11.1 Running a Spike Sorting Analysis ........................................................................................131
11.2 Identifying Units from the UI ...............................................................................................136
11.3 Adjusting the Spike Sorter Sensitivity...................................................................................141
11.3.1 Increasing the Sensitivity to find more Units..............................................................141
11.3.2 Avoiding Noise Units ................................................................................................143
11.4 Memory Issues ....................................................................................................................144
11.5 Distributed Spike Sorting .....................................................................................................145
11.5.1 Converting Raw Data to Units ..................................................................................145
11.6 Spike Sorting Algorithm ......................................................................................................147
11.6.1 Basic Principles..........................................................................................................147
11.6.2 Independent Component Analysis (ICA) ...................................................................148
11.7 Main Processing Steps .........................................................................................................149
11.7.1 Extract Regions of Interest ........................................................................................150
11.8 Extract Units from a Region of Interest ................................................................................151
11.8.1 Remove Redundant Units .........................................................................................154
11.9 Unit Quality Measures .........................................................................................................155
11.9.1 SNR ..........................................................................................................................155
11.9.2 Skewness..................................................................................................................155
11.9.3 Kurtosis ....................................................................................................................155
11.9.4 AmplitudeSD ............................................................................................................155
11.9.5 RSTD ........................................................................................................................156
11.9.6 Separability...............................................................................................................156
11.9.6 IsoIBg and IsoINN......................................................................................................156
12 References ...............................................................................................................................157
13 Support and Troubleshooting ...............................................................................................158
13.1 Troubleshooting..................................................................................................................158
13.2 Technical Support ...............................................................................................................159
14 Technical Specifications..........................................................................................................160
14.1 CMOS-MEA Chip................................................................................................................162
14.2 Test-CMOS-MEA.................................................................................................................163
14.3 IFB-Control Software……………………………………………………………………………..165
15 Contact Information ...............................................................................................................166
16 Index ........................................................................................................................................167

5
1 Important Safety Advice
Warning: Make sure to read the following advice prior to installation or use of the device
and the software. If you do not fulfil all requirements stated below, this may lead to
malfunctions or breakage of connected hardware, or even fatal injuries.
Warning: Always obey 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.
The product has been built to the state of the art and in accordance with recognized safety engineering
rules.The device may only
•be used for its intended purpose;
•be used when in a perfect condition.
Improper use could lead to serious, even fatal injuries to the user or third parties and damage to the
device itself or other material damage.
Warning: The device and the software are not intended for medical uses and must not be used
on humans. MCS assumes no responsibility in any case of contravention.
Malfunctions which could impair safety should be rectified immediately.
Grounding
This product is grounded through the grounding conductor on the power cord. To avoid electric shock,
the grounding conductor must be connected to earth.
Orient the Equipment Properly
Do not orient the equipment so that it is difficult to manage the disconnection device.
High Voltage
Electrical cords must be properly laid and installed. The length and quality of the cords must be
in accordance with local provisions.
Only qualified technicians may work on the electrical system. It is essential that the accident prevention
regulations and those of the employers' liability associations are observed.
•Each time before starting up, make sure that the power supply agrees with the specifications
of the product.
•Check the power cord for damage each time the site is changed. Damaged power cords should
be replaced immediately and may never be reused.
•Check the leads for damage. Damaged leads should be replaced immediately and may never
be reused.
•Do not try to insert anything sharp or metallic into the vents or the case.
•Liquids may cause short circuits or other damage. Always keep the device and the power cords dry.
Do not handle it with wet hands.

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Requirements for the Installation
Make sure that the device is not exposed to direct sunlight. Do not place anything on top of the device,
and do not place it on top of another heat producing device, so that the air can circulate freely.
Explanation of the Symbol used
Caution / Warning DC, direct current
1.1 Guarantee and Liability
The general conditions of sale and delivery of Multi Channel Systems MCS GmbH always apply.
They can be found online at
http://www.multichannelsystems.com/sites/multichannelsystems.com/files/documents/Terms and
Conditions.pdf Multi Channel Systems MCS GmbH makes no guarantee as to the accuracy of any
and all tests and data generated by the use of the device or the software. It is up to the user to use
good laboratory practice to establish the validity of his / her findings.
Guarantee and liability claims in the event of injury or material damage are excluded when they are
the result of one of the following:
•Improper use of the device.
•Improper installation, commissioning, operation or maintenance of the device.
•Operating the device when the safety and protective devices are defective and/or inoperable.
•Non-observance of the instructions in the manual with regard to transport, storage, installation,
commissioning, operation or maintenance of the device.
•Unauthorized structural alterations to the device.
•Unauthorized modifications to the system settings.
•Inadequate monitoring of device components subject to wear.
•Improperly executed and unauthorized repairs.
•Unauthorized opening of the device or its components.
•Catastrophic events due to the effect of foreign bodies or acts of God.
1.2 Operator's Obligations
The operator is obliged to allow only persons to work on the device, who
•are familiar with the safety at work and accident prevention regulations and have been instructed
how to use the device;
•are professionally qualified or have specialist knowledge and training and have received instruction
in the use of the device;
•have read and understood the chapter on safety and the warning instructions in this manual
and confirmed this with their signature.
It must be monitored at regular intervals that the operating personnel are working safely. Personnel
still undergoing training may only work on the device under the supervision of an experienced person.

7
2 Introduction
2.1 Welcome to the CMOS-MEA5000-System
Multi Channel Systems is proud to present the CMOS-MEA5000-System. Based on the complementary
metal-oxide semiconductor technology, it opens up new possibilities in electrophysiological research.
With more than 4000 recording sites, each of them sampled at up to 25 kHz, the chip allows extracellular
recordings at a very high spatio-temporal resolution. By including amplification on the chip itself, noise
is minimized and a high signal quality is guaranteed. Stimulation is provided via 1024 stimulation sites
included in the chip and the stimulus generator in the headstage.
The CMOS-MEA5000-System consists of three components, which are all designed to be efficient and
powerful, while maintaining a small footprint.
CMOS-Chip
The chip is based on complementary metal oxide semiconductor (CMOS) technology, facilitating fast,
high resolution imaging of electrical activity. The chip is equipped with a culture or slice chamber to
house your sample, while allowing the use of a microscope.
Headstage
The core of the system is the headstage. It samples the data coming from the chip at 25 kHz per channel.
Besides A/D conversion and amplification, the headstage also houses a three-channel stimulator. You can
freely design the stimulation patterns via software and select each of the 1024 stimulation sites.
Interface Board
The interface board IFB-C offers the USB 3.0 interface to transfer the recorded data to a computer.
Moreover, it has analog and digital in- and outputs for synchronization with other instruments.
Connect the headstage via iX cable to the interface board. Connect the interface board via USB-C
cable to the data acquisition computer. Connect the interface board to the power outlet. Ground
the interface board if necessary. Please use the ground socket on the rear panel of the IFB-C.
Computer with Software
The software CMOS-MEA-Control and CMOS-MEA-Tools are programmed specifically for the CMOS-
MEA5000-System. It facilitates a real-time activity overview on the complete chip with the ability to zoom
in and various tools to analyze the data.

8
3 Hardware
3.1 Headstage
There are three hardware components for the CMOS-MEA5000-System available, the headstage,
the interface board and the data acquisition computer. If necessary you can use a temperature controller
additionally.
For setting up and connecting the CMOS-MEA5000-System, please read the next chapter "Hardware
Setup" on page 16.
The headstage samples data coming from the 4225 sensors on the chip at 25 kHz per channel. Besides
A/D conversion and amplification, the headstage also houses a three-channel stimulator. You can freely
design three stimulation patterns via software and select each of the 1024 stimulation sites.
Data transfer is provided via iX cable from the headstage to the interface board. The USB-C cable
connection arranges fast data transfer from the interface board to the data acquisition computer.
Connect a temperature controller TC to the headstage, if necessary.
Insert the test model probe or the CMOS-MEA-Chip in correct orientation into the provided area in the
headstage. The round edge of the probe or MEA has to be in the front on the left side, when looking
directly to the open headstage. This way the CMOS-Control software displays the electrodes in columns
and rows as shown on the scheme below. Electrode No 1 is placed on the left lower round edge of the
chip and electrode No 4225 is placed in the upper right edge.

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3.2 Chip Orientation inside the Headstage
If you are stimulating with light or extra electrodes from outside the chip, or if the orientation of the tissue
is important, please be aware that the line of vision is from the headstage side where the connector to the
IFB is located.
3.3 CMOS-MEA Chip
The chip is based on complementary metal oxide semiconductor (CMOS) technology, facilitating fast,
high-resolution imaging of electrical activity. The chip is equipped with a culture chamber to house your
sample, while allowing the use of a microscope.
The CMOS-MEA array is an active device, in contrast to the passive MEAs. It needs to be powered up
and down properly, or it will be damaged.
Warning: Before opening the CMOS-MEA headstage for removing the CMOS-MEA chip, it is necessary
to power the chip down, otherwise the chip will be destroyed!
CMOS sensor arrays are light sensitive. During recording the sensors need constant light conditions.
This is easy to obtain by covering the CMOS array with an appropriate dark chamber “CMOS-DC”.
CMOS-DC CMOS-TH
Please use the CMOS tissue holder “CMOS-TH”to keep acute slices in place. Available for CMOS-MEA
chip SCA and SCB.

10
The CMOS-MEA chip has a 65 x 65 layout and is available with 16 μm or 32 μm interelectrode distance
(center to center). The electrode diameter is always 8 μm. Between the recording electrodes, there
is a grid of 32 x 32 bigger stimulation sites. Summarizing, you can record from 4225 electrodes and
stimulate your sample at 1024 sites. The chip is coated with a planar oxide, similar to glass, enhancing
the biocompatibility and biostability. Please see the electron micrograph of the CMOS-MEA chip surface
(NMI Reutlingen, Germany) and the schema of the chip below.
The 16 μm interelectrode distance chip offers the highest resolution. With the high number of electrodes,
you can record from a large surface (1 mm² @ 16 μm distance, 4 mm² @ 32 μm distance). Thereby,
you can see the signals from every single cell and even the signal propagation along an axon, while still
getting an overview on your complete sample.
Your data is sampled at up to 25 kHz per channel. Thus, no signal is lost - even axonal spikes are
displayed and recorded thoroughly. Together with the A/D conversion at 14 bit, the system ensures
accurate and precise data.

11
At the moment three types of culture chambers are available for CMOS-MEAs: One for cell cultures and
two for acute slices. The chips for acute slices need an external Ag/AgCl electrode to ground the bath.
This ground electrode is already integrated in the CMOS chip for cell cultures.
CC Culture chamber for cell cultures with lid.
SCB Slice chamber basic.
Additionally a CMOS-MEA chip with a SCA Slice chamber with advanced layout for laminar flow
is available.
The warranty of a CMOS-MEA chip is six months from the date of delivery.

12
3.4 Interface Board IFB-C
The multiboot interface board IFB-C facilitates operation of all MCS in vitro and in vivo headstages within
the entire 2100 amplifier solution suite. This suite includes: MEA2100-HS, Multiwell-MEA-HS, CMOS-
MEA-HS, MEA2100-Beta- Screen-HS, W2100-HS and ME2100-HS. The modular 2100 amplifier solution
suite design makes it easy to modify your lab equipment generally with modest hardware upgrade
investments.
Front Panel
SYNC Out / In
Two or more interface boards IFB-C can be daisy-chained by use of the SYNC Out / SYNC In connectors.
All daisy-chained interface boards run on the same clock – to allow perfectly synchronized recordings in
large settings.
Analog Channels
Up to eight Analog In channels are available via 10-pin connector. Please read chapter 10-Pin Connector
for Analog IN in the Appendix for more information about the pin layout.
The additional analog inputs are intended for recording additional information from external devices,
for example, for recording patch clamp in parallel to the MEA recording.
Analog Channels 1 and 2
Two of these eight analog channels (Analog In No 1 and No 2) are separately available via Lemo
connectors on the front panel of the interface board IFB-C.
Two Status LEDs
The status LEDs indicate the link status of HS 1 and / or HS 2. They light up when one or both headstages
are connected to the IFB-C interface board via iX-industrial cable.
Digital IN / OUT
A Digital IN / OUT for 16 digital in- and output bits is available (Honda-PCS-XE68LFD) on the rear panel
of the interface board. On the front panel four Digital IN and four Digital OUT bits are also accessible via
Lemo connector (DIG IN bit 0 to bit 3 and DIG OUT bit 0 to bit 3). The Digital OUT delivers TTL pulses with
3.3 V or 5 V. The voltage can be switched between these two voltages with the software IFB-Control,
please read chapter “IFB-Control” in the Appendix.

13
If access to more bits of the DIG IN / OUT channel is required, it is necessary to connect a Digital IN / OUT
extension Di/o board with a 68-pin standard cable. This Di/o board is available as optional accessory.
Ground
If an additional ground connection is needed, you can connect this plug with an external ground using
a standard common jack (4 mm).
Rear Panel
Toggle Switch On / Off
Toggle switch for turning the device on and off. The CMOS-MEA5000-System is switched to status "ON"
when the toggle switch is switched to the left. The device is switched "OFF" when the toggle switch
is switched to the right. If the system is "ON", and the device is connected to the power line, the Power
LED on the front panel of the interface board should light up. If not, please check the power source and
cabling.
Power
Connect the power supply unit here. This power supply powers both, the headstage and the interface
board of the CMOS-MEA5000-System. The device needs 24 V and 2.5 A / 65 W.
Ground
If an additional ground connection is needed, you can connect this plug with an external ground using
a standard common jack (4 mm).

14
Digital IN / OUT
A Digital IN / OUT for 16 digital in- and output bits is available via Honda-PCS-XE68LFD connector.
Please read chapter Digital IN / OUT Connector in the Appendix for more information about the pin layout
of the connector. The Digital IN / OUT connection accepts or generates standard TTL signals. The Digital
OUT delivers TTL pulses with 3.3 V or 5 V. The voltage can be switched between these two levels with
the software IFB-Control, please read chapter “IFB-Control” in the Appendix.
TTL stands for Transistor-Transistor Logic. A TTL pulse is defined as a digital signal for communication
between two devices. A voltage between 0 V and 0.8 V is considered as a logical state of 0 (LOW),
and a voltage between 2 V and 3.3 V or 5 V means 1 (HIGH).
The Digital OUT allows generating a digital signal with up to 16 bits and read it out, for example, by using
a Digital IN / OUT extension Di/o board. You can utilize this digital signal to control and synchronize other
devices with the MEA2100-Beta-Screen-System.
Bit 0 to 3 of the Digital OUT are separated and available as Lemo connector DIG OUT 0 to 3 on the front
panel of the interface board. So, the Di/o extension is only necessary if more than four trigger inputs or
outputs are needed.
The Digital IN can be used to record additional information from external devices as a 16 bit encoded
number. The Digital IN is most often used to trigger recordings with a TTL signal. The 16 bit digital input
channels is a stream of 16 bit values. The state of each bit (0 to 15) can be controlled separately. Standard
TTL signals are accepted as input signals on the digital inputs.
Warning: A voltage that is higher than +3.3 Volts or +5 Volts or lower than 0 Volts, that is, a negative
voltage, applied to the digital input would destroy the electronics. Make sure that you apply only TTL
pulses (0 to 3.3 V or 5 V) to the digital inputs.
Auxiliary Channels
Two reserve auxiliary channels are available for future use. They have no function at the moment.
Audio OUT
The "Audio OUT" function is not available for the CMOS-MEA5000-System.
DSP JTAG Connector
The JTAG connector is used to program the digital signal processor DSP for real-time feature.
This feature is not in use in CMOS-MEA5000-Systems.
HS / SCU
Sockets for connecting up to two CMOS-MEA-System headstages via iX-industrial cable(s), type B.
USB-C Connectors B and A
Both USB-C connectors are used to transfer the amplified and digitized data from all data channels and
the additional digital and analog channels to any connected data acquisition computer via USB-C cable.
Connector A corresponds with connector iX input 1, and connector B with iX input 2. If both iX inputs
are used, also both USB-C connections must be used. Both USB cables must be connected to different
USB-C ports of the computer, do not use an USB hub! Only use high grade USB-C cables, as provided
with the system.
Important: It is recommended to connect the USB-C cable direct to the USB 3.0 port of the computer.
Do not use an USB hub!

15
Data Acquisition Computer
The software CMOS-MEA-Control was programmed specially for the CMOS-MEA5000-System.
It facilitates a real-time activity overview on the complete chip with the ability to zoom in and various
tools to analyze the data. Please read chapter "CMOS-MEA-Control" for information about the software.
The data acquisition computer is provided by Multi Channel Systems MCS GmbH. The operation system
Windows ® 10 or 8.1 is necessary. Due to the huge amount of recorded data, a computer with low
performance may lead to performance problems; therefore, Multi Channel Systems provides an up-to-
date computer with USB 3.0 connection and Intel chip set. Use a SSP hard drive for recording and
a second hard drive for backup. At full frame sampling with maximum sampling rate the currently used
1TB SSD drive will hold about one hour of continuous recording only!

16
4 Hardware Setup
Please follow the instructions:
1. Connect the CMOS-MEA5000 amplifier via iX-industrial cable, type B to the IFB-C interface board.
Please use the plug in labelled with “1” on the back of the interface board.
2. Connect the IFB-C via power unit to the power outlet.
3. Connect the IFB-C via USB-C to the computer. Use the USB-C plug in labelled with “A”
on the backside of the interface board.
4. Connect the IFB-C via USB-C cable to the backside of the computer. It is mandatory to use
the designated USB 3.0 port, please see the picture below!
Important: It is necessary to connect the interface board IFB-C of the CMOS-MEA5000-System to an Intel
® USB 3.0 port. Otherwise, you risk data loss.
Please consider the error message when starting the CMOS-MEA-Control software for the first time.
Important: Make sure that all paths for recording files go to the SSD drive otherwise no recording is
possible!
5. Connect the temperature controller TC via USB 2.0 high speed cable to one of the USB 2.0 ports
and via power unit to the power outlet.
6. Connect the heating element of the CMOS headstage via provided cable to the temperature controller.

17
5 Installation of the Software
5.1 System Requirements
If you have purchased the CMOS-MEA5000-System with PC everything is preinstalled and tested. If you
purchase a system without a PC please make sure that the computer meets our specifications relating
processor, memory, hard disk, etc. Please contact Multi Channel Systems MCS GmbH or your local
retailer.
Software: One of the following Microsoft Windows ® operating systems is required: Windows 10 or 8.1,
64 Bit (English and German versions supported) with the NT file system. Other language versions may lead
to software errors.
Due to the amount of recorded data, a computer with low performance may lead to performance
problems; therefore, Multi Channel Systems MCS GmbH recommends an up-to-date computer.
Please contact MCS or your local retailer for more information on recommended computer hardware
specification.
Important: Because of the huge amount of acquired data (up to 220 MByte per second), make sure
that all paths for recording files go to the SSD drive, otherwise no recording is possible!
Please note that there are sometimes hardware incompatibilities of the data acquisition system and
computer components; or that an inappropriate computer power supply may lead to artefact signals.
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 CMOS-MEA-Control. These routines were
designed for use on office computers, but are not very useful for a data acquisition computer.
•Deselect "Windows Indexing Service" for data SSD and HD disks, the system hard drive is not
included.
•Switch off the sleep mode for displays and HD disks.
•Power Options: Power scheme: High performance. Never turn on system standby.
•Turn off "Optimize hard disk when idle", the automatic disk fragmentation.
•Turn off the Screen Saver and do not use a virus scanner during experiment.
•It is also not recommended to run any applications in the background when using CMOS-MEA-
Control. Remove all applications from the "Autostart" folder.
Important: Please make sure to have full control over your computer as an administrator. Otherwise,
it is possible that the installed software does not work properly.
Doubleclick the CMOS-MEA-Control.exe on the installation volume. The installation assistant will show
up and guide you through the installation procedure. Follow the instructions of the installation assistant.
Note: During installation, all drivers are installed and if necessary, the firmware of the CMOS-MEA5000
hardware is updated. Please do not interrupt the firmware update.

18
5.2 Testing the CMOS-MEA5000-System
Functional Tests of the CMOS-MEA5000-System with the Test Model Probe
Please read also the datasheet “Test-CMOS-MEA” in the Appendix. Insert the "Test Model Probe"
in correct orientation and close the headstage. The round edge of the Test-CMOS-MEA or the
CMOS-MEA chip has to be in the front on the left side when looking directly to the open amplifier.
The provided test model probe simulates a CMOS-MEA chip with a resistor of 100 kΩand a 10 p
capacitor between ground and each row of the 65 x 65 electrodes in the grid. It can be used for
testing the noise level of a CMOS-MEA5000-System, for a test of calibration and for testing the
internal stimulators.
CMOS-MEA test model probes and CMOS-MEA chips are active devices and must be switched on
and shot down properly, otherwise they might suffer damage.
Please click the MEA array icon in the "Data Source" window. CMOS chips must be calibrated before
each use. The calibration runs automatically and usually takes two to three minutes. Please do not
interrupt the process, until the final message "Finished automatic system calibration" appears. The
“Test CMOS-MEA” simulates the calibration of the chip.
The „ODD“ cable supports the odd-numbered channels and the „EVEN“ cable supports the even-
numbered channels. For the intention to check the noise level of a CMOS-MEA5000-System without
external signals, please connect the cable soldered to the „ODD“ connector to the input connector
of the even-numbered channels and the cable soldered to the „EVEN“ connector to the „BATH“ input.
Connected in this way, the signal input supports all 65 rows of the 65 x 65 layout of the CMOS-MEA
chip at a time and simulates also the calibration of the bath. Disconnect the "ODD" connector to see
the "EVEN" numbered electrodes only and vice versa to see the "ODD" numbered electrodes only.

19
Test of the internal Stimulators
The Test-CMOS-MEA probe is equipped with three additional connectors to test the internal stimulation,
„STG1“, „STG2“ and „STG3“. The stimuli are color coded in the CMOS-MEA-Control software:
Stimulus 1 is indicated in green color, Stimulus 2 is indicated in blue and Stimulus 3 in red color.
For testing a stimulator, please connect the cable of the "ODD" connector to the "EVEN" connector and
the open cable to one of the "STG" plug ins. Define a respective stimulus pattern in the "Stimulation"
window, for example a ramp with 100 ms on stimulator 1 (green), as shown on the screenshot above.

20
CMOS-MEA Chip
Please fill the CMOS-MEA chip with PBS and add an external reference electrode. CMOS sensors are light
sensitive. To record a stable baseline the CMOS-MEA array must maintain under stable light conditions,
which can easily be provided by covering the CMOS-MEA with the convenient dark chamber “CMOS-
DC”. Otherwise the signal will drift out of range by the effect of light.