Elements esca User Manual

esca

Elements Single Channel Amplifier

User’s Manual v1.2

February 2014

esca User’s Manual v1.2

CONTACTS

Elements s.r.l.

via Montalti, 42

47521 Cesena

ITALY

email: [e-mail]

web: www.elements-ic.com

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CONTENTS

INTRODUCTION ................................................................................................................ 4

Introduction to ESCA .................................................................................................................................. 4

HARDWARE SETUP ............................................................................................................. 4

Front Connections ...................................................................................................................................... 5

Rear Connections ....................................................................................................................................... 5

Tipical Experimental Setup ........................................................................................................................ 5

SOFTWARE GUIDE ............................................................................................................. 6

Requirements ............................................................................................................................................. 7

Installation .................................................................................................................................................. 7

Software Operating Procedure .................................................................................................................. 9

Graphical User Interface .......................................................................................................................... 10

ESCA Setup .............................................................................................................................................. 11

Digital Offset Compensation .................................................................................................................... 12

Statistic Data ............................................................................................................................................. 13

Trace Visualization ................................................................................................................................... 14

Save Data ................................................................................................................................................. 16

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INTRODUCTION

INTRODUCTION TO ESCA

ESCA (Elements Single Channel Amplifier) is a current measurement system entirely
contained in a USB stick designed for voltage clamp experiments.

Thanks to a custom-made microchip for low-noise current signal acquisitions, ESCA
achieves high performances in a very small size package.

The main features of ESCA are:

- two input current ranges: ±200 pA and ±20 nA;

- 4 selectable signal filters: 625 Hz, 1.25 kHz, 5 kHz and 10 kHz;

- very low noise:  80 fA rms at 625 Hz & < 400 fA rms at 10 kHz (open input);

- integrated voltage stimulus in the range of ±355 mV with 1mV resolution;

- SMB input coaxial connector. Several adapters available;

- small size (30x15x74mm);

- software included;

HARDWARE SETUP

ESCA is designed to be as simple as possible to connect to your various different
setups.

In order to obtain the best performance, the main things to be careful are parasitic
capacitances on the input and correct shielding of the overall hardware setup to avoid
the 50/60Hz line interferences and other electromagnetic interferences.

An adequate faraday cage must be used. The faraday cage should be large enough to
contain all your sensitive equipment and must be connected to the common ground.

Be careful to avoid ground loops by using a “star ground” connection.

Be careful to keep the input sensitive line as far as possible from the faraday cage walls
to limit the parasitic capacitances on the input as much as possible.

The following paragraphs describe all the connections and how to connect them in the
right way.

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FRONT CONNECTIONS

On the front of ESCA there is the connection for your Device Under Test (DUT).

This connector is a coaxial SMB male gold plated connector where the center contact is
the current measurement input and the outer contact is the reference voltage.

IMPORTANT: Do NOT short the reference to the ground.

REAR CONNECTIONS

On the rear of ESCA there are two connectors:

- mini-B female USB connector to connect to the PC through the included USB

cable;

- 2mm gold plated ground female connector for connecting the ESCA ground

to a Faraday cage;

TIPICAL EXPERIMENTAL SETUP

This picture shows how to correctly connect ESCA in a typical electrophysiology setup:

USB

Ground

LED

Reference

Input

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To obtain the best noise performances a particular care must be given to the shielding
with a metallic cage (Faraday cage) all around the experimental setup. In particular, it
is important to connect the Faraday cage to the ground connector placed on the rear of
ESCA.

In order to minimize the noise it is also important to minimize parasitic capacitances
between the input and the shielding by keeping the wires as short as possible and as
far as possible from the Faraday cage, including your Device Under Test (DUT).

With certain PC, there can be some issues with USB power supply that can introduce
noise and peaks on the acquired signal. In these cases we recommend to use a
powered USB 2.0 hub.

This is an example of a real setup for artificial lipid bilayer experiments:

SOFTWARE GUIDE

Elements Data Reader (EDR) is the control software for ESCA devices. It enables the
total control of ESCA devices features (such as set the data acquisition properties and
the control voltage) and enables the real time data visualization and data saving. Data
acquired by means of this custom software are handily readable by Matlab® and can

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be saved to be compatible with standard commercial software such as pClamp® from
Molecular Devices®.

IMPORTANT: The software must be installed BEFORE connecting the ESCA device
to the PC.

REQUIREMENTS

The minimum system requirements are:

 Dual core processor 1GHz or better
 1GB of RAM
 A free USB 2.0 port
 Windows XP / Vista / Seven / 8

INSTALLATION

To start the installation procedure, double click on the installation executable
EDR_setup_X.XX.exe (time limited evaluation version) or EDR_setup_X.XXu.exe

(unlimited version) and follow the instructions.

During the installation process you will be asked to install the FTDI driver needed to
communicate through USB to the ESCA devices.

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Click on Extract to prepare the installation of these drivers.

Then, start the FTDI installation by clicking on Next button and wait until installation
finishes.

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Now the Elements Data Reader software is correctly installed and ready to start.

After the software installation, you can connect the ESCA device to a free USB port. The
first time you connect the ESCA to your PC, you must wait for the new USB device
complete recognition.

NOTE: If the blue LED in the rear of ESCA doesn't light up or if you receive an installation
error, unplug ESCA from the USB and plug in again.

SOFTWARE OPERATING PROCEDURE

When started, the Elements Data Reader (EDR) software appears as in the following
picture:

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The first operation is to load a configuration file to initialize the software for the ESCA
devices.

This file contains all the necessary setups to communicate with the ESCA hardware.

The configuration file is loaded by clicking on the “Open Config” button. The
configuration file is ESCA_xxx.cfg where xxx is the firmware version of your ESCA
device. The configuration file is located in the EDR installation folder (usually
C:\Program Files (x86)\Elements Data Reader).

GRAPHICAL USER INTERFACE

After loading the config file, the GUI appears as follows:

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The upper section of the GUI presents the ESCA device specific commands (see the
“ESCA Setup” section for details).

Just below you can find some estimated statistic values on the input signal (see the
“Statistic Data” section for details), while on the right there are the controls to associate
an oscilloscope-like trace (beam) with a specific input signal in the visualization
window (in the case of ESCA devices, there is only one input channel available). See
the “Trace Visualization” section for details.

On the right there is an estimation of the input bitrate.

In the bottom you can find, in addition to the “Open Config” button already described

in the previous section, the following buttons:

 Connect – Starts the communication with the ESCA hardware.
 Show – Displays the data visualization window.
 Save – Save data.

In the bottom-right corner there is a drop-down list of the serial numbers of all the
recognized ESCA devices connected to the PC.

NOTE: Multiple instances of the software can run on the same PC enabling to control
several ESCA devices connected to the same PC. If more than one ESCA device are
connected, you must first choose the correct device Serial Number to be controlled.

To start acquiring data, click on the “Connect” button.

ESCA SETUP

The ESCA setup tab contains the following controls:

 Range
 Bandwidth
 Constant Control Voltage
 Digital Compensation
 Triangular Control Voltage
 ESCA reset

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The Range buttons enable to choose between two ranges:

 from -200 pA to +200 pA

or

 from -20 nA to + 20 nA

The Bandwidth buttons select the input signal bandwidth:

 10 kHz button: 10 kHz bandwidth, 20 kHz sampling rate
 5 kHz button: 5 kHz bandwidth, 10 kHz sampling rate
 1.25 kHz button: 1.25 kHz bandwidth, 2.5 kHz sampling rate
 625 Hz button: 625 Hz bandwidth, 1.25 kHz sampling rate

The value of the constant control voltage (Vc) applied at the ESCA input pin is
controlled with the “Vc Value” box in the following range:

 from -355 mV to +355 mV with 1mV steps

In order to be sure of the applied control voltage, a digital offset compensation
procedure must be followed. In the next section the digital compensation is described.

The “Triangular Wave” check box is used to force a 48 Hz triangular wave control
voltage of peak to peak amplitude of 118 mVpp. This voltage signal is used to estimate
the input capacitances as described in the “Statistic Data” section.

The “Reset” check box keep the ESCA device in reset mode. This function can be
useful to reset the digital offset compensation value to the initial value (see the “Digital
Offset Compensation” section for details).

DIGITAL OFFSET COMPENSATION

To compensate the voltage offset due to internal opamp offsets or unwanted electrode
potentials, ESCA has an internal calibration procedure that can be activated with the
“Digital Compensation” check box.

The compensation circuit, when activated, sets the Vc to 0 V and adds to it a variable
voltage in the range from -118 mV to +118 mV until the current is 0 A.

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In order to successfully compensate the offset, a conductive path must be present on
the input. Do NOT compensate the voltage offset with open input.

The compensation need only few seconds. To return to normal operation, UNCHECK
the “Digital Compensation” check box. The compensation value remains stored

internally and added to the Vc.

STATISTIC DATA

The Graphical User Interface of the EDR software includes some statistical data analysis
done in real-time during the current acquisitions.

These estimated statistic data are:

 Mean value
 Standard Deviation (STD)
 Equivalent input capacitance
 Equivalent input resistance
 Saturation

The mean and Std values are calculated in real-time. The input acquired data are split
in temporal windows whose length is dependent on the estimated input data bitrate
and memorized in a buffer. Then, the mean and std values are calculated on these
buffers.

When the user changes the bandwidth, there can be necessary to wait some time to
have valid estimated statistic data.

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The following instructions have to be followed to obtain capacitance and resistance
estimations.

Capacitance estimation:

 Activate the “Triangular Wave” check box;
 Set the best range between 200 pA and 20 nA (NOTE: for capacitance values

higher than about 17pF select the 20nA range in order to avoid amplifier
saturation);

 Check that the acquired current is a square waveform;
 Click on the “C estimation” button.

Resistance estimation:

 Be sure the “Triangular Wave” check box is NOT checked;
 Set a Vc value between 10 mV and 355 mV;
 Check that the acquired current is constant, greater than 0 A and not saturating

the amplifier;

 Click on the “R estimation” button.

The “Saturation” indicator means the input current exceeded the maximum or

minimum current value for the selected Range.

TRACE VISUALIZATION

The data visualization is based on a freeware dll written by Michael Bernstein (more
info on www.oscilloscope-lib.com).

Click on the “Show” button to activate the visualization window that displays the

acquired input current.

The visualization window enables to display up to 3 channel concurrently in a
oscilloscope like approach.

Each beam can be associated to a specific data channel in the EDR GUI. In the case of
ESCA devices, since there is only one channel available, the beams setup in the GUI
can be left unchanged.

In the bottom of the display window there are the buttons necessary to control the
visualization.

In particular, from left to right, these are the button functions:

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 Vertical zoom

NB: the unit of measurement depend on the selected Range. It is pA if the 200 pA range is
selected and nA if the 20 nA range is selected

 Horizontal zoom

NB: in the GUI there is the value of the time/DIV value, in ms/DIV, corresponding to the
horizontal zoom level

 Set vertical 0 point in the middle of the window

 Change the grid dimensions

 Change the vertical offset (shift)

 Change the horizontal offset (shift)

 Search for a channel

NB: useless with ESCA devices since they are single channel amplifiers. Do NOT use it.

 Return to the previous horizontal and vertical zoom

 Select the beam, or all the beams, for the zoom and shift commands

NB: useless with ESCA devices since they are single channel amplifiers. Do NOT use it.

 Activate the trigger function

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 Suspend the visualization window from receiving the input

data

NB: This feature can cause a software crash in systems with Windows 8.

SAVE DATA

The EDR software can save data in three file formats:

 Proprietary .DAT files - A binary format with data represented in single

precision values.

 Comma separated values .csv files - A simple text format with data represented

as text.

 Axon™ binary format v2 .abf files – The Axon™ file format used by commercial

pClamp® software from Molecular Devices®.

First, choose which format will be used by clicking on File->Preferences.

To start saving data, click on the “Save” button. The data are saved in the temporary
path set in the "Preferences" menu. Be careful to have enough disk space to save data.

When saving begins, a timer in the GUI starts and indicates the total saving time.

NOTE: You cannot change acquisition Range or Bandwidth while saving data.

To stop saving, click on the “Stop saving” button. You will be asked for a location
where data will be saved.

Saving can automatically stop after the amount of time set in the preferences menu.

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The EDR software creates a new folder in the location chosen by the user with the same
name of the saving files. In this new folder the EDR software creates some files:

 An header .txt file containing some ESCA setup information (Range, Bandwidth,

etc.).

 The saved data files.

The EDR software create a new data file every n minutes of acquisition to limit the
maximum file dimensions. n is set in the preferences menu. This feature is not available
when saving in .abf data format.

The proprietary .dat files can be handily read by Matlab® with the included function in
the ESCAread.m file located in the installation directory (usually C:\\Program Files

(x86)\Elements Data Reader).

Data samples are stored in standard 32 bit single precision format, little endian.

The ESCAread Matlab® function will ask you the location of the saved data files and the
data bandwidth.

The function returns in three vectors the data, Vc and time values.

To load saved data, just type in the Matlab® command windows:

[Data, Vc, Time] = ESCAread();

The data are in pA units if the selected range is 200 pA and in nA units if it is 20 nA.

Here is the ESCAread Matlab® function:

function [ data, vc, time ] = ESCAread( )
% edr_read
% Function to read data saved in binary format from the EDR software
%
% returns:
% data - An array of data, one channel in every column;
% vc - A vector reprensenting the command voltage Vc;
% time - The time vector;
%

% select data file
[filename, pathname] = uigetfile('*000.dat');

% check for valid data file name
if length(filename) < 9
display('Error: invalid file name');
exit
end
if ~strcmp(filename(end-7:end), '_000.dat')
display('Error: invalid file name');

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exit
end

% check number of files and their names
basefilename = filename(1:end-8);
files = dir(strcat(pathname, basefilename, '*.dat'));
N = length(files);

% read files
B = [];
for i = 1:N
fid = fopen(fullfile(pathname, files(i).name)); % open file for read
A = single(fread(fid, 'single')); % Array of single precision values
fclose(fid); % close file
B = [B;A];
end

% reshape data in an array with 2 columns (1 channels + vc)
C = reshape(B(1:2*fix(length(B)/2)), 2, []);
D = C';

% select sampling frequency
display('Select bandwidth:');
display('1) 625 Hz');
display('2) 1.25 kHz');
display('3) 5 kHz');
display('4) 10 kHz');
sel = input('select 1,2,3,4: ');
switch sel
case 1
OSR = 1024;
case 2
OSR = 512;
case 3
OSR = 128;
case 4
OSR = 64;
otherwise
display('Error: invalid selection');
exit
end
Fs = 1250000 / OSR;

% return arrays
data = D(:, 1);
vc = D(:, 2);
time = (0:(length(vc) - 1)) * (1 / Fs);

% plot data
subplot(2,1,1)
plot(time, data)
grid on
xlabel('Time [s]')
ylabel('I [pA]')
subplot(2,1,2)
plot(time, vc)
grid on
xlabel('Time [s]')
ylabel('Vc [mV]')

end

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