Sutter Instrument IPA User manual

One Digital Drive
Novato, CA 94949 USA
Voice: [phone] Web: www.sutter.com
Fax: [phone] Email: in[email protected]m
IPA™
Integrated patch amplifier
ELECTROPHYSIOLOGY
PATCH-CLAMP SYSTEM
WITH
SUTTERPATCH™SOFTWARE
Operation Manual
Rev. 1.0.6 (20160729)

INTEGRATED PATCH AMPLIFIER SYSTEM OPERATION MANUAL –REV.1.0.6 (20160729)
2
Copyright © 2016 Sutter Instrument Company. All Rights Reserved.
IPATM and SutterPatchTM are trademarks of Sutter Instrument Company.
Other brand names mentioned may be trademarks of other companies.

INTEGRATED PATCH AMPLIFIER SYSTEM OPERATION MANUAL –REV.1.0.6 (20160729)
3
DISCLAIMER
The IPA consists of one electronic amplifier with integrated digitizer and one headstage. The
purpose of the system is for the stimulation and measurement of cellular preparations. No other
use is recommended.
This instrument is designed for use in a laboratory environment. It is not intended for, nor
should it be used in human experimentation or applied to humans in any way. This is not a
medical device.
Do not open or attempt to repair the instrument.
Do not allow an unauthorized and/or untrained operative to use this instrument.
Any misuse will be the sole responsibility of the user/owner, and Sutter Instrument Company
assumes no implied or inferred liability for direct or consequential damages from this instru-
ment if it is operated or used in any way other than for which it is designed.
SAFETY WARNINGS AND PRECAUTIONS
Electrical
§Operate the IPA using 110 – 240 VAC, 50-60 Hz line voltage. This instrument is de-
signed for use in a laboratory environment that has low electromagnetic noise
and mechanical vibration. Surge suppression is recommended at all times.
Fuse Replacement: Replace only with the same type and rating:
Line Voltage: 110 – 240 VAC
Fuse
Rating
Manufacturer Examples
RoHS Compliant (Lead Free)
§
T2.0,
250V
Bussmann: GMC-2-R, S506-2A
Littelfuse: 239.002.P
Type: 5 x 20 mm glass tube, Medium Time Delay (Slow Blow), RoHS compliant.
Rating: T2.0A 250V (Time Delay, 2 Amps, 250 Volts)
Examples: Bussmann: GMC-2-R, S506-2A
Littelfuse: 239.002.P
§Avoiding Electrical Shock and Fire-related Injury
§Always use the grounded power cord provided to connect the system’s power
adapter to a grounded/earthed mains outlet (3-prong). This is required to protect
you from injury in the event that an electrical hazard occurs.
§Do not disassemble the system. Refer servicing to qualified personnel.
§To prevent fire or shock hazard do not expose the unit to rain or moisture.

INTEGRATED PATCH AMPLIFIER SYSTEM OPERATION MANUAL –REV.1.0.6 (20160729)
4
Operational
Failure to comply with any of the following precautions may damage this instrument.
§This instrument is designed for operation in a laboratory environment (Pollution
Degree I) that is free from mechanical vibrations, electrical noise and transients.
nOperate this instrument only according to the instructions included in this man-
ual.
nDo not operate this instrument near flammable materials. The use of any
hazardous materials with this instrument is not recommended and, if undertak-
en, is done so at the users’ own risk.
nDo not operate if there is any obvious damage to any part of the instrument.
Other
§Retain the original packaging for future transport of the instrument.
§Sutter Instrument reserves the right to change specifications without prior no-
tice.
§Use of this instrument is for research purposes only.
Handling Micropipettes
Failure to comply with any of the following precautions may result in injury to
the users of this instrument as well as those working in the general area near the in-
strument.
§The micropipettes used with this instrument are very sharp and relatively fragile.
Avoid contact with micropipette tips to prevent accidentally impaling yourself.
§Always dispose of micropipettes by placing them into a well-marked, spill-proof
“sharps” container.

INTEGRATED PATCH AMPLIFIER SYSTEM OPERATION MANUAL –REV.1.0.6 (20160729)
5
TABLE OF CONTENTS
DISCLAIMER.....................................................................................3!
SAFETY WARNINGS AND PRECAUTIONS .............................................3!
Electrical!............................................................................................................................................................................!3!
Operational!......................................................................................................................................................................!4!
Other!.....................................................................................................................................................................................!4!
Handling Micropipettes!..........................................................................................................................................!4!
1. INTRODUCTION .............................................................................8!
Overview!............................................................................................................................................................................!8!
Features!......................................................................................................................................................................................................!8!
Advanced Design!..................................................................................................................................................................................!8!
Software Feature Comparison!...........................................................................................................................!9!
1.1 Experiment Structure!....................................................................................................................................!10!
2. INSTALLATION ............................................................................14!
2.1 System Requirements!....................................................................................................................................!14!
2.2 SutterPatch System Environment!........................................................................................................!14!
2.3 Mounting Instructions!..................................................................................................................................!15!
2.4 Electrical Connections!..................................................................................................................................!15!
2.5 Install Hardware!...............................................................................................................................................!15!
Initial Set-Up!................................................................................................................................................................!16!
2.6 Install Software!..................................................................................................................................................!16!
2.7 INSTALL DRIVER!............................................................................................................................................!17!
2.8 Test System!............................................................................................................................................................!17!
3. HARDWARE OPERATION...............................................................20!
3.1 IPA Front Panel!.................................................................................................................................................!20!
3.2 IPA Rear Panel!...................................................................................................................................................!20!
3.3 IPA Control Panel!.............................................................................................................................................!21!
3.4 Peripheral I/O!......................................................................................................................................................!25!
3.5 External Amplifiers!.........................................................................................................................................!25!
3.6 External Digitizers!...........................................................................................................................................!26!
4. SOFTWARE OPERATIONS..............................................................26!
WINDOWS DIALOGS AND PANELS .....................................................26!
4.1 Dashboard Panel!...............................................................................................................................................!26!
4.2 Scope Window – Data Acquisition!.........................................................................................................!27!
Right-Click Menus!....................................................................................................................................................!36!
4.3 Scope Window – Membrane Test!............................................................................................................!36!
4.4 Scope Window – Free Run (Scope)!.......................................................................................................!36!
4.5 Scope Window - Data Analysis!.................................................................................................................!37!
Right-click!Menus!...........................................................................................................................................................!39!
4.6 Analysis Window!................................................................................................................................................!39!
4.7 3D View Window!................................................................................................................................................!40!
4.7.1 Axis Definitions!.....................................................................................................................................................................!40!
4.8 Layout Window!...................................................................................................................................................!42!

INTEGRATED PATCH AMPLIFIER SYSTEM OPERATION MANUAL –REV.1.0.6 (20160729)
6
4.9 Command Window!...........................................................................................................................................!42!
4.10 Log Window!........................................................................................................................................................!44!
Dialogs............................................................................................45!
4.11 Routine Editor!..................................................................................................................................................!45!
4.12 Routine Editor: Acquisition & Routine Parameters!.............................................................!52!
4.13 Routine Editor: Input Channels!..........................................................................................................!56!
4.14 Routine Editor: Output Channels & Waveform!........................................................................!56!
4.15 Routine Editor: Waveform Editor!.......................................................................................................!59!
4.16 Routine Editor: Real Time Measurements & Graphs!...........................................................!64!
4.17 Paradigm Editor..............................................................................................................................................!69!
4.18 Variables Window!..........................................................................................................................................!79!
4.19!Equation!Editor!.....................................................................................................................................................!80!
4.20 Data Navigator!.................................................................................................................................................!84!
4.21 Data Table!............................................................................................................................................................!86!
4.22 Routine Review!................................................................................................................................................!86!
4.23 Preferences!.........................................................................................................................................................!87!
4.24 Set Metadata!......................................................................................................................................................!90!
4.25 Review Metadata!............................................................................................................................................!92!
4.26!Menus!........................................................................................................................................................................!93!
4.27 Import/Export Data!.......................................................................................................................................!94!
5. APPLICATIONS ............................................................................95!
5.1 Data Acquisition!................................................................................................................................................!95!
5.2 Data Analysis!........................................................................................................................................................!96!
5.3 Voltage-Gated Currents!................................................................................................................................!96!
5.4 Ligand-Gated Currents!.................................................................................................................................!96!
5.5 Event Detection!..................................................................................................................................................!96!
5.6 Use Dependence!.................................................................................................................................................!97!
6. MAINTENANCE ............................................................................98!
7. TECHNICAL SUPPORT ..................................................................99!
APPENDIX A. Software license ............................................................................................ 100!
APPENDIX B. LIMITED WARRANTY ................................................................................ 101!
APPENDIX C. ACCESSORIES ............................................................................................ 102!
APPENDIX D. Fuse Replacement ........................................................................................ 103!
APPENDIX E. TECHNICAL SPECIFICATIONS ................................................................ 104!
E.1. IPA Amplifier!............................................................................................................................................................................!104!
E.2. Electrode Holder!.....................................................................................................................................................................!106!
E.3. Glossary of Terms!..................................................................................................................................................................!107!
E.4. Bioelectric Terminology!....................................................................................................................................................!107!
E.5. Software Limits!.......................................................................................................................................................................!107!
E.6. Hardware Limits!...................................................................................................................................................................!107!
APPENDIX F. Programming ................................................................................................ 109!
INDEX ..........................................................................................109!
TABLE OF FIGURES
Figure 1-1. SutterPatch execution paths............................................................................................ 11!

INTEGRATED PATCH AMPLIFIER SYSTEM OPERATION MANUAL –REV.1.0.6 (20160729)
7
Figure 2-1. Rear of IPA cabinet ........................................................................................................... 15!
Figure 2-2. Front of IPA cabinet .......................................................................................................... 16!
Figure 2-3. IPA Control Panel ............................................................................................................. 18!
Figure 2-4. Dashboard – Acquire Data ............................................................................................... 19!
Figure 2-5. Dashboard – Membrane Test........................................................................................... 19!
Figure 4-1. SutterPatch Dashboard. ................................................................................................... 26!
Figure 4-2 Scope View of SutterPatch ................................................................................................ 28!
Figure 4-3 Signals ................................................................................................................................. 29!
Figure 4-4. Signal Display Mode ......................................................................................................... 29!
Figure 4-5. Axis magnification............................................................................................................. 30!
Figure 4-6. Axis scroll bar..................................................................................................................... 31!
Figure 4-7. Auto scale all axes ............................................................................................................. 32!
Figure 4-8. Amplitude Meters.............................................................................................................. 33!
Figure 4-9. Reanalysis View of Scope Window .................................................................................. 37!
Figure 4-10. Navigation Pane. ............................................................................................................. 38!
Figure 4-11. 3D View and axis definition. .......................................................................................... 41!
Figure 4-12. Routine Editor ................................................................................................................. 45!
Figure 4-13. Routine Settings and sub-items..................................................................................... 49!
Figure 4-14. Acquisition Parameters Menu ....................................................................................... 52!
Figure 4-15. New Routine..................................................................................................................... 57!
Figure 4-16. Waveform Editor ............................................................................................................. 60!
Figure 4-17. Time Analysis Graph ...................................................................................................... 65!
Figure 4-18. Paradigm Editor .............................................................................................................. 69!
Figure 4-19. Data Table Example ....................................................................................................... 86!
Figure 4-20. SutterPatch Routine Review.......................................................................................... 87!
TABLE OF TABLES
Table 1-1. Software Comparison.............................................................................................................9!
Table 1-2. Software Terminology......................................................................................................... 13!
Table 4-1. Routine Editor Buttons ...................................................................................................... 49!
Table 7-1. IPA cables and receptacles/connectors............................................................................ 106!

INTEGRATED PATCH AMPLIFIER OPERATION -MANUAL –REV.1.0.6 (20160729)
8
1. INTRODUCTION
Welcome to a new era in Patch-Clamp Technology! Our passion is creating the next generation of elec-
trophysiology research instrumentation. With over two centuries of combined experience from across
the patch-clamp industry, our experienced team has designed a new microelectrode amplifier-
recording system that is powerful enough to satisfy experienced patch-clampers, yet easy-to-use for
new entrants, such as Molecular Biologists.
Sutter Instrument Company is a leading manufacturer of innovative precision instrumentation in the
Neuroscience field. We have a worldwide reputation for the highest quality and performance of pipette
pullers, micromanipulators, light sources and wavelength switchers. We now bring this same com-
mitment to the next generation of patch-clamp instrumentation.
Overview
Features
§Single program for data acquisition, data analysis and amplifier control
§Sophisticated data file structure with context retention and metadata capabilities
§Both online and offline data analysis
§Complex experimental control
Advanced Design
The IPA™ Integrated Patch Amplifier is the world’s first fully integrated microelectrode patch-
clamp system, which minimizes and streamlines your experimental setup. All of the electron-
ics and cabling used in stimulating, monitoring, compensating and recording from cells are in-
tegrated by design into a single-board instrument, the IPA.
The accompanying SutterPatch™ software brings the controls and displays for full-featured
data acquisition, data analysis, and graphics/layout together into a single unified program, in-
cluding a software control panel for direct access to all of the IPA amplifier functions.
The SutterPatch software was developed in the powerful Igor Pro 7 system environment. Igor
Pro, by WaveMetrics, Inc., is a data collection, management and analysis platform with a rich
set of built-in functions and routines for scientific programs.
From concept to production, from hardware to software, the IPA was designed as a fully inte-
grated computer-controlled patch-clamp amplifier-recording system. Your immediate benefits
are an affordable, easier-to-use, easier-to-setup, more robust, and more flexible patch-clamp
system for your electrophysiology experiments.

INTEGRATED PATCH AMPLIFIER OPERATION -MANUAL –REV.1.0.6 (20160729)
9
Software Feature Comparison
The SutterPatch program is a full-featured electrophysiology software package. In spite of a number
of conceptual similarities that help shortening the training, there are several major differences in how
the SutterPatch software compares to the Axon Instruments conventional electrophysiology software,
and some smaller differences compared to the HEKA electrophysiology software:
Table 1-1. Software Comparison
Topic
Sutter
Instrument
Axon
Instruments
HEKA
Elektronik
Sutter
Advantages
Software
Programs
SutterPatch
pCLAMP:
Clampex, Clampfit;
MultiClamp 700B
Commander
PATCHMASTER,
FITMASTER
A single program
for amplifier con-
trol, data acquisi-
tion, data man-
agement and data
analysis
Data Files
One “experiment”
data file (*.pxp)
for all data record-
ings per cell or per
day
One data file
(*.abf) per protocol
execution. Multi-
ple data files be-
longing to the
same recording
have no intrinsic
connection.
One “bundle” data
file (*.dat) for all
data recordings per
day or a longer pe-
riod
All acquisition
controls and con-
texts saved with
data in a compre-
hensive
experiment file
Flow
Control
Paradigms: com-
plex conditional
links
Sequencing Keys:
simple "go to" links
Protocols:
complex
conditional links
Create sophisticat-
ed assays and ex-
perimental
pathways
Sampling
Rates
Differing input
and output rates
Same input and
output rates
Same input and
output rates
Flexible acquisi-
tion parameters
for data through-
put and data stor-
age concerns
Command
Waveform
50 “segments” per
sweep
10 "epochs" per
sweep
Unlimited
"segments" per
sweep
Extended resolu-
tion of the com-
mand waveform

INTEGRATED PATCH AMPLIFIER OPERATION -MANUAL –REV.1.0.6 (20160729)
10
1.1 Experiment Structure
Experiment:
An Experiment is the highest-level structure in the SutterPatch world. An Experiment file (*.pxp)
can encompass all SutterPatch activity for the entire day, such as instructions (Paradigms),
settings, data acquisition parameters (Routines), recorded data (Series), program history and
comments. During reanalysis, data can be included from multiple experiments.
Some users may prefer to start a new Experiment for each new preparation, or even each new
cell they record. To avoid clutter, it is recommended not to collect data from more than one day
in a single Experiment file.
Paradigm:
A Paradigm is a sequence of control instructions in an Experiment. Every Experiment contains at
least one Paradigm.
Multiple Paradigms can exist in a Paradigm “pool”. To acquire data, a Paradigm runs one or
multiple Routines.
Paradigms can contain simple or sophisticated control structures using a rich set of operators.
Some of the operations include conditional processing via if-then statements, nested loops, user-
defined variables and hardware commands.
Paradigm Data:
The collection of all data points and metadata event tags acquired during the execution of a
paradigm is referred to as Paradigm Data. A copy of the paradigm is stored as part of the
Paradigm Data and enables repetition of the Paradigm the same way it was originally executed.
Routine:
A Routine is the set of data acquisition and online data analysis parameters that control input and
output channel timing, triggering, command waveforms, leak subtraction and display.
Multiple Routines can be held in a Routine “pool” for rapid access and execution.
Series (= Routine Data):
Acquiring data produces a Series composed of sweeps of data from all input signals. Multiple
runs of a Routine produce multiple Series of data. All Series are automatically stored in the
Experiment file.
In a planned Experiment, running a Paradigm will automatically execute any included Routines.
However, if a Routine is manually executed while no Paradigm is running, an “auto-triggered”
Paradigm is started;this default Paradigm ensures that each Series is associated with a Paradigm
in the context of an Experiment. See Figure 1-1