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− | <title>Hardware</title>
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− | <div id="example">
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− | <div class="pusher">
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− | <img class="ui medium sticky image" src="//2016.igem.org/wiki/images/d/d1/T--Slovenia--logo.png">
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− | <a class="item" href="//2016.igem.org/Team:Slovenia/Protease_signaling/Logic">
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− | <i class="chevron circle left icon"></i>
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− | <b>Logic</b>
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− | </a>
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− | <a class="item" href="#ach" style="margin-left: 10%">
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− | <i class="selected radio icon"></i>
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− | <b>Achievements</b>
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− | <a class="item" href="#mot" style="margin-left: 10%">
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− | <b>Motivation</b>
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− | <a class="item" href="#mod" style="margin-left: 10%">
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− | <b>MODUSON</b>
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− | </a>
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− | <a class="item" href="#rel" style="margin-left: 10%">
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− | <b>Realizations</b>
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− | <b>Evaluation</b>
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− | <b style="margin-left: 12%">of the device</b>
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− | </a>
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− | <a class="item" href="#set" style="margin-left: 10%">
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− | <i class="selected radio icon"></i>
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− | <b>Set-up</b>
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− | <br />
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− | <b style="margin-left: 12%">for experiments</b>
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− | </a>
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− | <a class="item" href="//2016.igem.org/Team:Slovenia/Model">
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− | <b>Modeling of ultrasound</b>
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− | </a>
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− | </div>
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− | </div>
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− | <div class="article" id="context">
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− | <div class="main ui citing justified container">
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− | <h1 class="ui left dividing header"><span id="ach" class="section"> </span>Ultrasound
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− | controlling device</h1>
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− | <div class="ui segment" style="background-color: #ebc7c7; ">
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− | <ul>
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− | <li><b>Implementation of 90 W ultrasonic amplifier for pulsed cells stimulation.</b>
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− | <li><b>Optimization of developed system in a given frequency range around 310 kHz.</b>
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− | <li><b>User friendly controlling interface of device.</b>
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− | <li><b>Capability of providing 7 kPa of pressure 4 mm from ultrasonic transducer.</b>
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− | </ul>
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− | </div>
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− | </div>
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− | <div class="ui segment">
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− | <h4><span id = "mot" class = "section"> </span></h4>
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− | <p>The ultrasound (US) wave interacts with tissue and reflects back depending on the
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− | properties of the tissues such as velocity of sound in the tissue and its density, which
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− | can be modeled using <a href="https://2016.igem.org/Team:Slovenia/Model">wave
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− | equation.</a> Higher frequencies have better resolution (shorter wavelengths) but
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− | cannot penetrate as deep into the tissues. In diagnostic ultrasound frequencies above 1
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− | MHz are used. For better tissue penetration frequencies of interest for our purposes are
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− | between 0.3 to 1 MHz yielding sufficient resolution and penetration at the same time
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− | <x-ref>Speed2001</x-ref>
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− | . Latest studies show that it is possible to use pulsed ultrasound for neurostimulation,
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− | ultrasound therapy such as treatment of pain and the repair of various tissues, however
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− | without clear knowledge which receptors or cell types we are targeting, and what is the
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− | mechanism of the ultrasound stimulation effects
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− | <x-ref>Vasquez2014</x-ref>
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− | .
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− | </p>
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− | </div>
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− | <h1><span class="section"> </span>Results</h1>
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− | <div class="ui segment">
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− | <div>
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− | <h3><span id="mod" class="section"> </span>MODUSON - Generating ultrasonic power
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− | pulses for cell stimulation</h3>
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− | <p>For the simple setup of the ultrasonic stimulation of cells we initially used ultrasonic
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− | baths (<ref>1</ref>) that are used to clean the laboratory equipment, small devices to clean jewelry or
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− | ultrasonic cell disruptors, which however offer little control over the intensity,
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− | frequency or pulse shapes and numbers of repetitions and are not appropriate to monitor
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− | activation of mechanosensors under the fluorescence microscope. However, one member of
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− | the team is a student of electrical engineering and this was the right challenge for
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− | him.
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− | </p>
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− | <div style="float:right; width:100%">
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− | <figure data-ref="1">
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− | <img src=" https://static.igem.org/mediawiki/2016/3/32/T--Slovenia--5.1.15.png">
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− | <figcaption><b>Different experiment configurations.</b><br/>
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− | <p style="text-align:justify">Testing homogeneity of pressure in each well with a plate immersed in the
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− | ultrasonic bath.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− | <p>For the generation of specific shapes of ultrasound pulses researchers usually use a
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− | setup consisting of two signal generators (one for switching on and off the train of US
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− | pulses and the other one to produce the sinusoidal signal of suitable frequency). This
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− | signal is further fed to the amplifier and then to the ultrasonic transducer.
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− | Furthermore, an ultrasonic sensor is required to evaluate and control the magnitude of
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− | the ultrasound. Usually a hydrophone is used in combination with an amplifier and an
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− | oscilloscope. This setup is complex to establish and difficult to use. Therefore, the
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− | goal of a part of the iGEM 2016 group (student of electrical engineering) was to develop
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− | a device (named Moduson), which would be capable of providing appropriate signals
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− | required to perform specific ultrasonic experiments in a single apparatus and as such
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− | easy to use. The research and development of the device was performed in the Laboratory
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− | for Bioelectromagnetics at the Faculty of Electrical Engineering, University of Ljubljana under
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− | the supervision of prof. dr. Dejan Križaj and a company Noeto.</p>
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− |
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− | </div>
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− | <div>
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− | <h3><span id="rel" class="section"> </span>The basic requirements for the device and
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− | realizations</h3>
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− | <h5>Adaptability</h5>
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− | <p>The device should be designed to be as flexible as possible in order to be capable of
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− | delivering a wide range and different shapes of stimulation signals to stimulate cells
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− | under the microscope, cells in a petri dish, cells in a microplate immersed into a bath
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− | and to stimulate animals. In order to fulfill this requirement we selected a dedicated
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− | embedded measurement card Red Pitaya acting as an embedded computer. This embedded
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− | device is based on Linux system and can be completely customized to the user’s needs.
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− | Furthermore, it can be Wi-Fi controlled so the final application is based on modern
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− | programming tools such as JavaScript, C++, HTML, etc. The final application is basically
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− | a web page, accessible with any computer capable of the Wi-Fi connection. This
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− | application gives complete control of all stimulation parameters and operation of the
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− | device. Another advantage of the platform used is its capability of simple integration with
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− | Matlab through so-called SCPI commands, usually used in the instrumentation for easy
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− | control and data acquisition making the device perfect research and development tool.
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− | Simple example of SCPI commands in Matlab for pulsed bursts is shown below:</p>
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− | <div style="float:left; width:100%">
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− | <figure>
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− | <img src=" https://static.igem.org/mediawiki/2016/b/b6/T--Slovenia--5.1.5.png">
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− | </figure>
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− | </div>
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− |
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− | <p style="clear:both">On the
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− | <ref>2</ref>
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− | a typical sequence of a stimulation signal constructed of a set number of sine waves of
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− | defined frequency that is repeated for required number of times with selected repetition
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− | period is shown.
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− | </p>
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− | <div style="float:left; width:100%">
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− | <figure data-ref="2">
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− | <img src="https://static.igem.org/mediawiki/2016/6/6e/T--Slovenia--5.1.6.png ">
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− | <figcaption><b>Signal parameters.</b><br/>
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− | <p style="text-align:justify">Parameters that can be set for a typical stimulation signal.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− |
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− | <h5>Simple graphical user interface</h5>
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− | <p>Users of the device do not need to be computer experts and do not need to have knowledge
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− | on the signal generators, amplifiers and oscilloscopes. Therefore, the motivation was to
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− | design and develop a simple user-friendly graphical interface with all the relevant
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− | parameters that need to be set in order to run the experiments from the Web page. To
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− | accomplish this, dedicated software was written that enables users to design and run the
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− | experiment and evaluate the results. <ref>3</ref> presents a developed user interface. On the right side (US burst settings -> STIMULATION
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− | PULSE) we can set parameters, such as the amplitude of the signal, frequency and number
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− | of sine waves. Below these settings, repetition parameters of the signal (PULSE
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− | REPETITION) such as the number of pulse repetitions and its frequency can be set. When
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− | all parameters are set, the signal can be previewed by clicking the SHOW BURST button.
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− | The pulse sequence is initiated with the START button. The acquired signal from
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− | hydrophone is seen on the main plot. At the top of the interface, there are options to
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− | export the image of a graph and csv data of the acquired signal. Chosen values of
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− | parameters can also be saved for the next use of the device.
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− | </p>
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− | <div style="margin-left:auto; margin-right:auto; width:50%">
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− | <figure data-ref="3">
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− | <img onclick="resize(this);"
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− | src=" https://static.igem.org/mediawiki/2016/b/bf/T--Slovenia--5.1.7.png">
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− | <figcaption><b>Application interface.</b><br/>
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− | <p style="text-align:justify"> Web based interface used for setting of the signal parameters.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− |
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− | <h5 style="clear:both">Signal amplifier</h5>
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− |
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− | <div style="width: 33%; float:left;">
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− | <figure data-ref="4">
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− | <img class="ui medium image" onclick="resize(this);"
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− | src=" https://static.igem.org/mediawiki/2016/7/7e/T--Slovenia--5.1.8.png">
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− | <figcaption><b>Simulation scheme.</b><br/>
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− | <p style="text-align:justify">Scheme used in LT Spice simulations.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− | <div style="width: 33%; float:left;">
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− | <figure data-ref="5">
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− | <img class="ui medium image" onclick="resize(this);"
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− | src="https://static.igem.org/mediawiki/2016/3/3b/T--Slovenia--5.1.9.png ">
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− | <figcaption><b>Model of transducer.</b><br/>
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− | <p style="text-align:justify">Equivalent model of ultrasonic transducer based on a BVD model.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− | <div style="width: 33%; float:left;">
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− | <figure data-ref="6">
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− | <img class="ui medium image" onclick="resize(this);"
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− | src=" https://static.igem.org/mediawiki/2016/0/0a/T--Slovenia--5.1.10.png">
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− | <figcaption><b>Moduson.</b><br/>
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− | <p style="text-align:justify">Constructed device with a simple interface; an ON/OFF button, a BNC output for
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− | the transducer and a button to trigger stimulation pulses. The pulses can also
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− | be triggered directly through the Web interface.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− | <p style="clear:both;"></p>
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− | <p>We built the circuitry with real elements on a prototype board where several additional
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− | alterations were required, as the real elements do not have ideal characteristics as the
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− | ones included in the simulation. Another challenge was the design of a suitable
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− | transformer to increase the voltage amplitude of the signal. The transformer is also
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− | required to operate as an impedance transformer. Lowering impedance of the ultrasonic
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− | transducer enables higher current levels and consequently higher power values.</p>
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− | <p>Once a suitable signal is generated, it needs to be amplified from a signal level
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− | (amplitude of 2 V) to several hundred volts or even above 1000 V, which poses a serious
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− | engineering challenge. For this purpose, we first designed a circuitry on a conceptual
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− | level and simulated it with LT Spice (<ref>4</ref>). In the simulations an electric model of a transducer was considered as a combination
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− | of capacitors, inductors and resistors wired in parallel (<ref>5</ref>). This model enables simulation of ultrasonic transducers with several resonant
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− | frequencies. Simulations show that our device can reach the power at transducer around
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− | 92W, which is close to the measured 86W in the real system.
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− | </p>
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− | </div>
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− | <div>
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− | <h3><span id="eva" class="section">nbsp;</span>Evaluation of the developed device
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− | </h3>
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− |
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− | <p>Functionality of the Moduson was first tested without any connected load. <ref>7</ref> presents a typical output measured with an oscilloscope for a signal of frequency 310
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− | kHz.
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− | </p>
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− |
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− | <div style="float:left; width:100%">
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− | <figure data-ref="7">
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− | <img src="https://static.igem.org/mediawiki/2016/5/58/T--Slovenia--5.1.2.png ">
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− | <figcaption><b>Typical output signal without load.</b><br/>
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− | <p style="text-align:justify">Amplitude of acquired signal depends on the winding of transformer.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− |
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− | <p>Developed device was tested with several transducers with resonance frequencies ranging
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− | from 300 kHz up to 1 MHz. Most experiments were performed with an unfocused transducer
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− | Olympus V318-SU (<ref>8</ref>) with a waterproof case, allowing it to be used in <i>in vitro</i> experiments.
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− | </p>
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− |
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− | <div style="float:left; width:50%">
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− | <figure data-ref="8">
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− | <img src="https://static.igem.org/mediawiki/2016/f/fe/T--Slovenia--5.1.11.png ">
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− | <figcaption><b>Ultrasound transducer V318-SU.</b><br/>
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− | <p style="text-align:justify">Handy waterproof case allowed us to use the transducer in most experiments.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− | <div style="float:left; width:50%">
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− | <figure data-ref="9">
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− | <img src="https://static.igem.org/mediawiki/2016/2/2e/T--Slovenia--5.1.4.png ">
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− | <figcaption><b>Electric power of ultrasonic transducer before and after
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− | compensation.</b><br/>
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− | <p style="text-align:justify">Electrical power with compensation was significantly increased with serial
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− | compensation.</p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− |
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− |
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− | <p>
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− | <ref>9</ref>
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− | presents measured electric power using the transducer V318-SU. After partial
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− | compensation of reactive part, the measured real power reached 86 W. This result
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− | exceeded the set requirements.
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− | </p>
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− |
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− | <p>With compensation, voltage was considerably increased at contacts of transducer and
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− | reached around 900Vpp as shown in <ref>10</ref>.
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− | </p>
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− | <div style="float:left; width:100%">
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− | <figure data-ref="10">
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− | <img src="https://static.igem.org/mediawiki/2016/3/3d/T--Slovenia--5.1.1.png ">
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− | <figcaption><b>Voltage at input of a transducer V318-SU.</b><br/>
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− | <p style="text-align:justify">Transducer requires relative high voltage to operate properly.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− |
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− | <p>We measured the emitted ultrasonic pressure indirectly with a hydrophone RP 31l shown in <ref>11</ref>. This hydrophone has a sensitivity of 50mV/100kPa at a frequency of 310kHz. It can be
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− | connected directly to the oscilloscope input to detect the pressure of the ultrasonic
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− | waves. Pressure measured 4 mm from the transducer reached 7 kPa which gives the
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− | intensity of 33 W/cm<sup>2<sup>.</p>
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− |
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− | <div style="float:left; width:50%">
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− | <figure data-ref="11">
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− | <img src="https://static.igem.org/mediawiki/2016/e/e5/T--Slovenia--5.1.12.png ">
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− | <figcaption><b>Hydrophone RP 31l.</b><br/>
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− | <p style="text-align:justify">Calibrated hydrophone used to measure pressure.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− |
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− | <p style="clear:both">Example of an output signal measured by a hydrophone is presented in
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− | the <ref>12</ref>.
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− | <p>
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− |
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− | <div style="float:left; width:100%">
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− | <figure data-ref="12">
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− | <img src=" https://static.igem.org/mediawiki/2016/b/b8/T--Slovenia--5.1.3.png">
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− | <figcaption><b>Voltage signal detected using the hydrophone.</b><br/>
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− | <p style="text-align:justify">With calibration data, we can determine pressure which corresponds to acquired
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− | voltage amplitude.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− | <p style="clear:both;">
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− | </p>
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− | </div>
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− | <div>
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− | <h3><span id="set" class="section">nbsp;</span>Set-up for experiments with ultrasonic
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− | pulses</h3>
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− |
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− | <p>After we successfully tested the Moduson device, we aimed to design measurement set-up
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− | for stimulation of cells cultivated in plastic 6-well plates, which allows insertion of
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− | the ultrasound transducer. In order to ensure repeatable conditions in every experiment
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− | the position of a transducer was fixed with a suitable holder. Several models of holders
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− | were designed for different experimental configurations and a 3D-printer was used to
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− | fabricate a dedicated holder (<ref>13</ref>). This allowed positioning of the transducer at the fixed height above the bottom of a
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− | well (<ref>14</ref>), which was crucial due to the series of maximal and minimal intensity of generated
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− | pressure.
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− | <p>
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− | <div style="float:left; width:50%">
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− | <figure data-ref="13">
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− | <img src="https://static.igem.org/mediawiki/2016/8/88/T--Slovenia--5.1.13.png ">
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− | <figcaption><b>3D printer.</b><br/>
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− | <p style="text-align:justify">Printing a holder for the ultrasonic transducer that we used for a 6-well plate.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− |
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− | <div style="float:left; width:50%">
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− | <figure data-ref="14">
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− | <img src=" https://static.igem.org/mediawiki/2016/e/ea/T--Slovenia--5.1.14.png">
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− | <figcaption><b>Ultrasound based experiments on the microscope.</b><br/>
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− | <p style="text-align:justify">Ultrasonic transducer with a 3D printed holder in a 6-well plate.
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− | </p>
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− | </figcaption>
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− | </figure>
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− | </div>
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− |
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− | <p style="clear:both;">
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− | </p>
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