Team:TU Eindhoven/Microfluidics/Methods/Informal Information Evening

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Latest revision as of 16:59, 13 October 2014

iGEM Team TU Eindhoven 2014

Informal Information Evening

On Friday the 26th of September we hosted an open evening for friends, family and other interested parties to inform them of the essence of synthetic biology, its opportunities and challenges and our iGEM project. During the evening we gave two presentations, one on synthetic biology in general and one on our project specifically. To see whether or not we helped our guests better understand synthetic biology we also took various tests, which were part of a social experiment. Below some pictures are shown in order to give an impression of the evening.

Next, the lecture on synthetic biology in general was given by Glenn
Cremers and a quick test for the audience was led by Bram Somers
and Minke Nijenhuis.

The reception area, where guests could answer the questions of the first
test, while enjoying a a cup of coffee or tea.

Between the two lectures ,there was a break in which the public was asked to make another test.

The lecture on the iGEM competition, our project and the underlying
mechanisms was given by Anke Boschman. The microfluidics part was
covered by Leroy Tan and Bram Somers explained some application
scenarios of our Click Coli system.

We would like to thank the Institute for Complex Molecular Sciences
(ICMS) for providing us with a location for this great evening.

In our opinion the evening was quite successful and we are glad we could share our enthusiasm for synthetic biology with the community. We hope we have presented synthetic biology and our iGEM project in a way that was understandable to everyone present the evening of the 26th of September. If there are questions about the content of the lectures, please contact the presenters of the lectures.

iGEM Team TU Eindhoven 2014

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-<figure style="float:right;margin-right:0;">
-<img id='Fig1' src="https://static.igem.org/mediawiki/2014/b/be/TU_Eindhoven_Modeling4.png" width="500" style="display: inline-block; border: 4px solid #00BAC6; padding: 4px; background: #222; margin-bottom: 10px;">
-<figcaption style="font-size:18px;color:#CCCCCC;">Figuur 1. Used sample image.</figcaption>
-</figure>
                    <h2>Informal Information Evening</h2>
                    <p>On Friday the 26th of September we hosted an open evening for friends, family and other interested parties to inform them of the essence of synthetic biology, its opportunities and challenges and our iGEM project. During the evening we gave two presentations, one on <a href="" target="_blank">synthetic biology in general</a>  and one on <a href="" target="_blank">our project specifically</a>. To see whether or not we helped our guests better understand synthetic biology we also took various tests, which were part of a <a href="">social experiment</a>.  Below some pictures are shown in order to give an impression of the evening.</p>
-<p>The program has the following steps: find and count the droplets, then find and count the cells in the droplets and finally create a histogram of the results (number of droplets with 0 cells, with 1 cell, with 2 et cetera). By adding up the histograms of multiple images you get a view of how the cells are divided over the droplets.</p>
+<figure style="float:right;margin-right:0;margin-left:0">
+<img id='Fig1' src="https://static.igem.org/mediawiki/2014/2/28/TU_Eindhoven_IIE2.jpg" width="525" style="display: inline-block; border: 4px solid #00BAC6; padding: 4px; background: #222; margin-bottom: 10px;">
+<figcaption style="font-size:18px;color:#CCCCCC;">Next, the lecture on synthetic biology in general was given by Glenn <br> Cremers and a quick test for the audience was led by Bram Somers <br> and Minke Nijenhuis.</figcaption>
+</figure>
-<figure style="float:left;margin-left:0;">
+<figure style="float:left;margin-left:0;margin-right:0">
-<img id='Fig2' src="https://static.igem.org/mediawiki/2014/a/a1/TU_Eindhoven_Modeling5.png" width="500" style="display: inline-block; border: 4px solid #00BAC6; padding: 4px; background: #222; margin-bottom: 10px;">
+<img id='Fig1' src="https://static.igem.org/mediawiki/2014/2/24/TU_Eindhoven_IIE1.jpg" width="525" style="display: inline-block; border: 4px solid #00BAC6; padding: 4px; background: #222; margin-bottom: 10px;">
-<figcaption style="font-size:18px;color:#CCCCCC;">Figuur 2. Results after EdgeDetect</figcaption>
+<figcaption style="font-size:18px;color:#CCCCCC;">The reception area, where guests could answer the questions of the first <br> test, while enjoying a a cup of coffee or tea.</figcaption>
 </figure>
-<h3>Droplet Detection</h3>
+<figure style="float:right;margin-right:0;margin-left:0">
-<p>To detect the cells <i>EdgeDetect</i> (a function of Mathematica using gradient methods) is used followed by a dilation to make the edges clearer (<a href="#Fig2">Figure 2</a>).</p>
+<img id='Fig1' src="https://static.igem.org/mediawiki/2014/d/de/TU_Eindhoven_IIE3.jpg" width="1085" style="display: inline-block; border: 4px solid #00BAC6; padding: 4px; background: #222; margin-bottom: 10px;">
+<figcaption style="font-size:18px;color:#CCCCCC;">Between the two lectures ,there was a break in which the public was asked to make another test.</figcaption>
+</figure>
-<p>This results in clusters of pixels, all the pixels that are connected with only black pixels. The program then looks for the clusters bigger than 2000 pixels and smaller than 6000 pixels (<a href="#Fig2">Figure 3</a>).</p>
+<figure style="float:right;margin-right:0;margin-left:0">
+<img id='Fig1' src="https://static.igem.org/mediawiki/2014/0/07/TU_Eindhoven_IIE4.jpg" width="525" style="display: inline-block; border: 4px solid #00BAC6; padding: 4px; background: #222; margin-bottom: 10px;">
+<figcaption style="font-size:18px;color:#CCCCCC;">The lecture on the iGEM competition, our project and the underlying <br> mechanisms was given by Anke Boschman. The microfluidics part was <br> covered by Leroy Tan and Bram Somers explained some application <br> scenarios of our Click Coli system. </figcaption>
+</figure>
-<h3>Parameters of Droplets Detection</h3>
+<figure style="float:left;margin-left:0;margin-right:0">
-<p>The parameters of this function are chosen so they have a very low false positive, because a false positive means a non-existing droplet and thus false data.  A false negative only lowers the sample size, which can be increased by analyzing more images.</p>
+<img id='Fig1' src="https://static.igem.org/mediawiki/2014/8/83/TU_Eindhoven_IIE5.jpg" width="525" style="display: inline-block; border: 4px solid #00BAC6; padding: 4px; background: #222; margin-bottom: 10px;">
+<figcaption style="font-size:18px;color:#CCCCCC;">We would like to thank the Institute for Complex Molecular Sciences <br> (ICMS) for providing us with a location for this great evening.</figcaption>
-<figure style="float:right;margin-right:0;">
-<img id='Fig3' src="https://static.igem.org/mediawiki/2014/a/aa/TU_Eindhoven_Modeling6.png" width="500" style="display: inline-block; border: 4px solid #00BAC6; padding: 4px; background: #222; margin-bottom: 10px;">
-<figcaption style="font-size:18px;color:#CCCCCC;">Figuur 3. Results of selecting clusters</figcaption>
 </figure>
-<h3>Bacterial Cell Detection</h3>
+<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-<p>The program is now at the point where it has to count the number of cells in the droplets. Using the droplets from the edgedetect picture, erosion with value 1 is performed (resulting with the deletion of before in closing of the image). This makes sure the cells connected to the borders of the droplet are loose, the program deletes the border components so it only finds cells. The program uses <i>EnclosingComponentCount</i> instead of <i>count</i> now because a lot of cells became empty circles to get the results.
-<br><br>
-The results for this image are 9 false positives and 11 false negatives on a total of 93 cell in 126 droplets. Because some droplets had multiple false positives or false negatives the next step to improve this number is selecting to droplets better.
-</p>
-<figure style="float:left;margin-left:0;">
-<img id='Fig4' src="https://static.igem.org/mediawiki/2014/8/87/TU_Eindhoven_Modeling_Histogram.jpg" width="500" style="display: inline-block; border: 4px solid #00BAC6; padding: 4px; background: #222; margin-bottom: 10px;">
-<figcaption style="font-size:18px;color:#CCCCCC;">Figuur 4. Histogram of the example image</figcaption>
-</figure>
-<h4>Bibliography</h4>
+<p>In our opinion the evening was quite successful and we are glad we could share our enthusiasm for synthetic biology with the community. We hope we have presented synthetic biology and our iGEM project in a way that was understandable to everyone present the evening of the 26th of September. If there are questions about the content of the lectures, please contact the presenters of the lectures.</p>
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