Plexon Optogenetic Controller User manual

Stimulator 2.0 April 2011
Plexon Inc
6500 Greenville Ave. Suite 700
Dallas Texas 75206
United States of America
Tel:
214-369-4957
Fax:
214-369-1775
E
-mail: [e-mail]
www.plexon.com
Optogenetic Controller December 2012
Optogenetic Controller

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Optogenetic Controller
User’s Guide December 2012
CAUTION: THIS OPTOGENETIC CONTROLLER IS NOT FOR USE IN HUMANS
CAUTION: READ THE ENTIRE MANUAL BEFORE ATTEMPTING TO OPERATE THIS EQUIPMENT
Plexon Inc Proprietary
The information contained herein is the property of Plexon Inc. and it is proprietary and restricted
solely to assist Plexon Inc. customers.
Neither this document nor the contents may be disclosed, copied, revealed or used in whole or in
part for any other purpose without the prior written permission of Plexon Inc. This document must
be returned upon request of Plexon Inc.
The information contained in this document is subject to change without notice. Plexon Inc.
reserves the right to make changes in equipment design or components as progress in engineering
or manufacturing may warrant.
This user’s guide is PN 08-06-A-56-P11
This user’s guide refers to:
Hardware PN 08-06-A-04
Firmware PN 08-06-A-32
Software version 1.0.0
Copyright © 1983-2012 Plexon Inc, All Rights Reserved
® Plexon is a registered trademark of Plexon Inc.
Printed in the United States of America

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Table of Contents
1Getting Started..........................................................................................6
2Introduction..............................................................................................6
3System Requirements ...............................................................................6
4System components..................................................................................7
5Installation................................................................................................8
5.1 Software Installation ................................................................................................................................ 8
5.1.1 Browse to the \Optogenetic Contrller\Radient_x64 or \Radient_x86 folder on
the USB flash drive depending on if you have a 64 or 32 bit operating system .....................8
5.1.2 Right-click the file Radientx86v1Setup.exe or Radientx64v1Setup.exe and select
Run as Administrator to begin the installation process. On some computers, you will get
a warning:...............................................................................................................................................................8
5.1.3 Click Yes or Run to continue. The welcome screen appears:............................................8
5.1.4 Read and accept the Plexon End User License Agreement ...............................................9
5.1.5 You will be asked to confirm where the files will be stored: ............................................9
5.1.6 When the installation begins, it may take a couple of minutes before the
progress bar begins moving across the window. This is especially true in Windows 7:....9
5.1.7 An Opal Kelly FrontPanel USB Driver Setup window will pop up. ................................9
5.1.8 Accept the Opal Kelly License Agreement..............................................................................10
5.1.9 Click Finish When the Opal Kelly Driver Setup is complete...........................................10
5.1.10 Click Finish in the Plexon Radiant installation window...............................................10
5.1.11 The computer will have to be restarted to complete the installation....................10
5.2 Hardware Installation............................................................................................................................11
5.2.1 Connect the AC power cord between the AC outlet and the power supply.............11
5.2.2 Connect the DC power cord between the power supply and the Optogenetic
Controller. ............................................................................................................................................................11
5.2.3 Connect the USB cable between the Optogenetic Controller and the computer. 11
5.2.4 Connect the BNC cable between the Optogenetic Controller channel 1 and the
Oscilloscope.........................................................................................................................................................11
5.3 Turning on the power for the first time .........................................................................................12
5.3.1 Flip the power switch to the on position. The LED next to the switch on the end
of the Optogenetic Controller should illuminate. ..............................................................................12
5.3.2 The first time you turn the stimulator on a “Found New Hardware” balloon will
appear in the lower right hand corner of the computer screen. In Windows 7, the

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balloon changes from “Installing device driver software” to “Opal Kelly XEM6001”. In
Windows XP, the Found New Hardware Wizard will appear. Choose Install the software
automatically. After it is finished, the balloon will change to “Your new hardware is
installed and ready to use.”..........................................................................................................................12
6Getting Started........................................................................................13
6.1 Overview .....................................................................................................................................................13
6.2 Operational Flowchart...........................................................................................................................14
6.3 Launching the Radiant software........................................................................................................15
6.4 Using manual mode to use the controller......................................................................................15
6.5 Starting and Stopping Stimulation....................................................................................................16
6.6 Defining a pattern with a .txt file.......................................................................................................18
6.7 Loading a pattern from a .txt file .......................................................................................................18
6.8 Verifying the output on an oscilloscope.........................................................................................20
6.9 Using Different Scaling Options.........................................................................................................20
7GUI Function Reference ..........................................................................21
7.1 Status.............................................................................................................................................................21
7.2 Output Device............................................................................................................................................21
7.3 Output Mode .............................................................................................................................................. 21
7.4 Current or Voltage Limit.......................................................................................................................22
7.5 Pattern Source...........................................................................................................................................22
7.5.1 Manual Mode ......................................................................................................................................22
7.5.2 File............................................................................................................................................................22
7.5.2.1 Creating a stimulation pattern file.......................................................................................22
7.6 Repetitions and Count ...........................................................................................................................22
7.7 Trigger Options......................................................................................................................................... 23
7.7.1 Software Triggering ........................................................................................................................23
7.7.2 Digital Input Triggering ................................................................................................................23
7.7.2.1 Edge Triggering.............................................................................................................................23
7.7.2.2 Level Triggering.............................................................................................................................23
7.7.2.3 DI Polarity Positive.......................................................................................................................23
7.7.2.4 DI Polarity Negative.....................................................................................................................24
7.8 File Load Settings / File Save Settings.............................................................................................24
7.9 View............................................................................................................................................................... 24
7.10 Window........................................................................................................................................................24

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7.11 Help................................................................................................................................................................ 24
8Input and Output Connectors..................................................................25
8.1 Power In.......................................................................................................................................................25
8.2 Digital In ......................................................................................................................................................25
8.3 USB 2.0 .........................................................................................................................................................25
8.4 Current or Voltage Output connectors............................................................................................26
8.5 Status LEDs.................................................................................................................................................26
8.5.1 Device......................................................................................................................................................26
8.5.2 I (on) V (off) .........................................................................................................................................26
8.5.3 Running .................................................................................................................................................26
8.5.4 Non-Zero ...............................................................................................................................................26
8.6 Digital Out ...................................................................................................................................................27
8.7 Stimulation Cables...................................................................................................................................27
9Sample Arbitrary Waveform Pattern Files ...............................................27
10 Optogenetic Controller Limitations .........................................................28
10.1 Latency between digital input and voltage output ....................................................................28
10.2 Synchronization of multiple Controllers........................................................................................29
10.3 LED Flashes when changing from voltage to current mode ..................................................30
11 Specifications ..........................................................................................31

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1Getting Started
Before using your Optogenetic Controller, please check www.plexon.com/downloads.html for any
software updates.
2Introduction
The Plexon®Optogenetic Controller is a 4-channel current or voltage output device. It has 4
individually programmable channels that can be configured from a host computer using the Radiant
graphical user interface software or configured from user-written applications by means of a
software development kit (SDK). The maximum output of the Controller is up to 1100mA in current
mode or 5V in voltage mode. User defined output limits may be defined with 8-bit precision and
output waveforms may be defined with 8-bit resolution within those output limits.
Playback of pulses and arbitrary stimulation waveforms may be initiated from the host PC or
triggered in response to external digital inputs. Each channel has a dedicated start and stop digital
inputs that may be used to initiate and halt stimulation. Each channel also has four dedicated
digital outputs to signal to other devices the precise time when stimulation events are occurring.
Thank you for purchasing this Plexon product. We hope you are pleased with every aspect of it.
Please do not hesitate to contact us if you have any questions.
3System Requirements
A modern personal computer running Windows 7 or Windows XP with a free USB 2.0 port and 1 GB
of memory is required to operate the system.

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4System components
When you receive your Plexon Optogenetic Controller, confirm that you have the following pieces:
1. USB memory with software & drivers Plexon
2. AC power cord (7.5 ft)* Volex 17250 10 B1
3. Power Supply Plexon 08-06-A-37
4. USB Cable (2m) Monoprice 5438
5. Optogenetic Controller Plexon 08-06-A-04
6. Color-coded Insulated BNC Cables (4) Plexon 06-03-A-04-CCLL
* International customers: The stimulator power supply has an International Electrotechnical
Commission (IEC) 60320 C14 inlet for AC power (shown below). The AC power cord supplied with
the stimulator has an IEC 60320 C13 connector and a NEMA 5-15 plug compatible with the AC wall
outlets in North America. Users in other regions must supply a power cord with an IEC 60320 C13
connector and a plug that is compatible with the AC wall outlets in the region of use.
1
2
3
4
5
6

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5Installation
Read the entire installation section before proceeding with the installation. Follow the installation
steps in the order that they are presented. Install the software first, followed by the hardware. Do
not connect the controller to an implant until you have read the entire manual.
5.1 Software Installation
Read the entire Software Installation section before proceeding with any of the steps.
5.1.1 Browse to the \Optogenetic Contrller\Radient_x64 or \Radient_x86 folder on the USB flash
drive depending on if you have a 64 or 32 bit operating system
5.1.2 Right-click the file Radientx86v1Setup.exe or Radientx64v1Setup.exe and select Run as
Administrator to begin the installation process. On some computers, you will get a warning:
5.1.3 Click Yes or Run to continue. The welcome screen appears:
If the software is already installed, then the welcome screen gives you the option to repair
(re-install) or remove the software as shown on the right above. If the software is not
already installed, then the welcome screen shown above on the left appears.
Click Next to continue.

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5.1.4 Read and accept the Plexon End User License Agreement
Click Next to Continue
5.1.5 You will be asked to confirm where the files will be stored:
Click Next to continue.
5.1.6 When the installation begins, it may take a couple of minutes before the progress bar begins
moving across the window. This is especially true in Windows 7:
5.1.7 An Opal Kelly FrontPanel USB Driver Setup window will pop up.

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Click Next
5.1.8 Accept the Opal Kelly License Agreement
5.1.9 Click Finish When the Opal Kelly Driver Setup is complete.
5.1.10 Click Finish in the Plexon Radiant installation window
5.1.11 The computer will have to be restarted to complete the installation.

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5.2 Hardware Installation
Read the entire Hardware Installation section before proceeding with any of the steps.
An oscilloscope is highly recommended for viewing the output of the channels in voltage mode.
5.2.1 Connect the AC power cord between the AC outlet and the power supply.
5.2.2 Connect the DC power cord between the power supply and the Optogenetic Controller.
5.2.3 Connect the USB cable between the Optogenetic Controller and the computer.
5.2.4 Connect the BNC cable between the Optogenetic Controller channel 1 and the Oscilloscope.

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5.3 Turning on the power for the first time
5.3.1 Flip the power switch to the on position. The LED next to the switch on the end of the
Optogenetic Controller should illuminate.
5.3.2 The first time you turn the stimulator on a “Found New Hardware” balloon will appear in
the lower right hand corner of the computer screen. In Windows 7, the balloon changes
from “Installing device driver software” to “Opal Kelly XEM6001”. In Windows XP, the
Found New Hardware Wizard will appear. Choose Install the software automatically. After
it is finished, the balloon will change to “Your new hardware is installed and ready to use.”
Windows 7: Windows XP:

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6Getting Started
This section introduces the basic functions of the Optogenetic Controller and guides you through
basic operation using the voltage mode. Voltage mode is intended to be used to control lasers with
a 0-5V control input. The current mode functions similarly for controlling LEDs, but it is more
difficult to quantify the output without a light meter. It is highly recommended that you work
through this section before attempting to do any type of stimulation. Note that you will need an
oscilloscope to see the output.
6.1 Overview
Every optogenetic stimulation protocol begins with the definition of the stimulation pattern. The
graphical user interface (GUI) provides a means for manually setting the output value or loading a
stimulation pattern from a user-created text file. Once defined, the stimulation pattern is
downloaded into the controller memory for playback. Playback can be initiated from the GUI, SDK,
or in response to a digital input to the controller hardware.

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6.2 Operational Flowchart
Start Radiant
Software
Set LED or
LASER Mode
Set Max Curent,
Voltage, or
Power
Pattern
Manual
Enter Desired
Current or
Voltage
Pattern
File
Browse to File
No File Header
Enter Info With Header
Set Number of
Repetitions
Start
Stimulation
Pattern

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6.3 Launching the Radiant software
Make sure all of the Optogenetic Controllers are connected to the computer and turned on. Up to
four controllers can be used with a single computer. Then launch the Radiant software by double
clicking on the desktop icon.You should see the factory default graphical user interface as shown in
the figure below. Note that the number of controllers that are connected will determine the
number of tabs in the bottom left of the screen. Also, the LEDs on the end panel of the controller
will indicate the device number 1~4.
Hint: You may load the factory default configuration at any time by clicking File – Restore Factory
Settings.
Note that if the USB cable is not connected to the controller or if the controller power is turned off
when the software is started, the software will open but there will be no window to input
stimulation parameters, as seen on the left below. If you see the window on the right and your
stimulator is connected, it is possible that your layout has changed. Go to Window – Layout – Reset
to Default Layout.
6.4 Using manual mode to use the controller
The fastest and easiest way to use the controller is in manual mode. This is the mode that the
software will start in by default the first time the software is run. If it is not in manual mode, you
can select it by clicking the drop down menu next to Pattern Source.

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Begin by using a BNC cable to connect the output marked CH 1 to an oscilloscope. Next, set the
Output Device to Laser and the Voltage Limit to 5000mV. Then click in the box below Manual Mode
to and move the slider to 1000 (mV).
Hint: Fine incremental changes can be made to the slider value using the up and down arrow keys
or the scroll wheel on your mouse.
When you press the start button for channel 1 in the upper left, the output voltage will change to
1V.
Once the channel is running, you can adjust the slider to change the output voltage. The output will
remain at the set voltage until you stop the channel or change the value.
6.5 Starting and Stopping Stimulation
There are two ways to start playing a stimulation pattern: with the host PC through software and
with a hardware digital input. Note that a pulse started from software can be stopped with a digital
input and vice versa. In software, until a pattern for a channel has been defined, the start button in
the top left of the interface is grayed out. As soon as the pattern has been selected, the start button
becomes active. At that point, the channel can be triggered to start. To initialize stimulation from
the software, you can click the start button for the individual channel. Alternatively, the start all
button (to the right of channel 4’s start button) can be clicked and every channel that has been
configured will start at the same time. Once clicked, the start button changes functionality to
become a stop button.
In hardware there are start and stop TTL-compatible digital inputs for each channel. Inputs should
range from 0 – 5 V. Inputs <0.8V are logic “0” and >2.0V are logic “1”. The pinout for the Digital In
connector is shown below.
1– Start 1
3– NC
5– Start 2
7– NC
9 – Start 3
11 – NC
13 – Start 4
15 – NC
17 – Gnd
19 – Gnd
2– Stop 1
4– NC
6– Stop 2
8– NC
10 – Stop 3
12 – NC
14 – Stop 4
16 – NC
18 – Gnd
20 – Gnd

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The digital inputs can be operated in two different modes. To select the mode, click the drop down
menu next to DI Mode at the top of the screen.
The first mode is called Edge mode. In this case, a rising edge on the start pin initiates stimulation,
and a rising edge on the corresponding stop pin stops stimulation. If the stop input comes in the
middle of a stimulation pattern, the pattern will be cut short. Stimulation will also stop if the
pattern plays to completion. This is illustrated below.
The second mode is called Level mode. In this mode, the stimulation pattern starts when the Start
input transitions from 0 to 1, and continues until the pattern is complete or the Start input
transitions from 1 to 0. This is illustrated below.
As before, if the Start digital input goes low in the middle of a pattern, the pattern will be cut short.
A start signal that occurs after a pattern has been cut short will resume playback of the pattern.
When a stimulation pattern plays to completion, the Radiant software will automatically re-load the
pattern in preparation for another start signal. However, the process of detecting the end of the
pattern and re-loading the pattern takes some time and it may be on the order of 100 ms before the
pattern is ready to be triggered again.
There are two ways to set the polarity of the digital inputs: Positive and Negative. These can be
accessed from the drop down menu DI Polarity at the top of the screen.
In Positive mode, the controller responds to a rising edge if the inputs are in edge mode, or to a
logic 1 in level mode. This is the more common method of communicating through TTL. In
Negative mode, the controller responds to a falling edge if the inputs are in edge mode, or to a logic
On
Current/Voltage Output
Start (Level Trigger Mode)
On
Current/Voltage Output
Start (Edge Trigger Mode)
Stop (Edge Trigger Mode)

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0 in level mode. Care should be taken when changing polarity as it is possible to inadvertently start
stimulation. For example, the digital inputs are pulled low, so if the polarity is set to negative with
no input connected all channels that are ready will start when the polarity is changed from positive
to negative.
6.6 Defining a pattern with a .txt file
Stimulation patterns can be defined in simple text files using any text editor software (Microsoft
Word, Notepad, etc.). More advanced users can programmatically create files using software such
as Matlab or Labview.
The text file is simply a list of amplitudes that is updated every 100µs. To maintain a value longer
than 100µs, the value is repeated. Several sample files are included in the installation package.
The amplitude units can be binary (0-255), mA, mV, or mW. The user specifies the units when
loading the text file.
6.7 Loading a pattern from a .txt file
First set the Output device as LASER, output mode as Voltage (mV), and Voltage Output Limit (mV)
to 5000.
Begin by selecting File from the Pattern Source drop down menu.
Next click on the folder in the field next to Load from File.
A dialog box will pop up. There are two types of files (.opt and .txt). A .opt file has a header that
defines stimulation parameters such as units, while a .txt file is just a series of amplitudes.

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Select the file pulse_bursts.txt that is located at C:\Plexon Data\Sample Pattern Files. Note that the
pattern files are Read Only. To change them, first copy and rename the original and then remove
the Read Only flag by right clicking the file name and selecting Properties from the drop down. One
of the dialog boxes below will appear depending on whether LASER or LED is selected for the
Output Device.With Laser selected, you will see the dialog box on the left.
Next you will select the units. Binary is a value from 0-255 which outputs a value from 0-max.
Voltage is represented in mV, Light Power is represented in mW, and Current in mA. Select Voltage.
If your output mode is in mV or mA, you should not select Light Power as your file’s units.
Likewise, if your output mode is in mW, you should not select Voltage or current as your
file’s units.
After you select the units the channel is ready and the start button becomes active. A preview will
appear on the left.
Hint: You can load a .txt file (with no header information) and then save it back as an .opt file
including header information based on the current software settings for the selected channel by
clicking on the button next to the Start All button.
The pattern stored in the file can be repeated a finite number of times or repeated continuously.
This is set in the fields below Load from file. Note that if the pattern is repeated, the first value in
the file will immediately follow the last value with no gap. If your pattern defines a series of pulses,
you will probably want to add some zeros at the end the pattern to maintain a constant pulse “rate”
during repeated playback. For this example select Continuous.
After the file has been loaded start the channel by clicking the start button at the top of the GUI.

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6.8 Verifying the output on an oscilloscope
Before connecting the output to an oscilloscope, confirm that the channel is in voltage output mode.
There are two ways to do this. The GUI should say Laser – Voltage and the LED on the end panel
below the text that says I (on) V (off) should be off.
Hint: If the channel is not playing but the voltage is still ~1.25V, the channel is in current mode. In
current mode, the LED is held at a voltage just below the turn-on threshold so that it can be turned
on more quickly when stimulation starts.
The output for the Pattern1_pulse_bursts.txt file that was loaded in LASER – mV mode should look
like the image below. Note that the scaling is 100mV per division and 1 second per division.
6.9 Using Different Scaling Options
The Optogenetic Controller fundamentally outputs either a 0-5V signal to control a laser or a 0-
1100mA signal to directly power an LED. The Radiant software allows patterns to be specified in
voltage or current, but some users may prefer to specify their stimulation pattern in terms of light
output. By inputting the amount of light produced at the maximum current, a linear interpolation is
performed. The software then calculates the amount of current or voltage required to generate any
light output. As an example, if a given LED outputs 10mW of light at 300mA, this information can
be used to calculate how much current is needed to output a desired amount of light of 7mW. This
calculation is transparent to the user.
In order to find the light output at the max current, the entire system should be assembled
(Optogenetic controller – BNC cable – LED module – Optical patch cable – Optical fiber implant).
User Input
Max Current = 300mA
Light = 10mW
User Request
Light = 7mW
Calculates 210mA