Team:Aachen/Collaborations/Freiburg

From 2014.igem.org

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We designed the app to be easy to use: A user can simply open the app
We designed the app to be easy to use: A user can simply open the app
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{{Team:Aachen/FigureFloat|Aachen_Collaboration-FRScreenshot1.png|title=Step 1: Start the app|width=170px}}
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{{Team:Aachen/Figure|Aachen_Collaboration-FRScreenshot1.png|title=Step 1: Start the app|width=170px}}
...read through very brief instructions...
...read through very brief instructions...
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{{Team:Aachen/FigureFloat|Aachen_Collaboration-FRScreenshot2.png|title=Step 2: Start scanning|width=170px}}
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{{Team:Aachen/Figure|Aachen_Collaboration-FRScreenshot2.png|title=Step 2: Start scanning|width=170px}}
...and start scanning for datamatrixes!
...and start scanning for datamatrixes!
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{{Team:Aachen/FigureFloat|Aachen_Collaboration-FRScreenshot3.png|title=Step 3: Aim for datamatrixes in the wild|width=170px}}
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{{Team:Aachen/Figure|Aachen_Collaboration-FRScreenshot3.png|title=Step 3: Aim for datamatrixes in the wild|width=170px}}
In the small picture you can see how the frames are pre-processed to be recognized by the ZXing datamatrix recognition algorithm. As soon as the algorithm finds a datamatrix, the string value is decoded and displayed to the user:
In the small picture you can see how the frames are pre-processed to be recognized by the ZXing datamatrix recognition algorithm. As soon as the algorithm finds a datamatrix, the string value is decoded and displayed to the user:
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{{Team:Aachen/FigureFloat|Aachen_Collaboration-FRScreenshot3.png|title=Step 4: Displaying the decoded text|width=170px}}
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{{Team:Aachen/Figure|Aachen_Collaboration-FRScreenshot3.png|title=Step 4: Displaying the decoded text|width=170px}}
== Outlook ==
== Outlook ==

Revision as of 19:13, 15 October 2014

AcCELLoMatrix with Team Freiburg

At the iGEM meetup in Munich in May , members of both of our teams realized that our projects share a common objective: Analyzing 2-dimensional, visual signals. For the following months, we stayed in contact and developed a concept to encode information in 384-well plates in the form of data matrix codes.

At the beginning of September, Michael spontaneously took a train to Freiburg and we met face-to-face for several hours to exchange details on our cooperation and general iGEM experiences.

Aachen FR-collaboration group photo.jpg
Spontaneous group photo
Freíburg iGEMers and Michael (right) meeting to discuss our cooperation

Data Matrix Masks for illumination

We decided to use masks to locally induce the cells in 384-well plates in a data matrix pattern. To enable us to quickly design masks for different data to be encoded, we wrote a software to easily generate SVG-files for a laser cutter.

Aachen DataMatrixMaskDesigner.png
Making a datamatrix mask
Upon entering a string, the software predicts if the datamatrix will fit into a 384-well plate.

After a string has been entered in the designer, an SVG-file can be saved and used for laser cutting the mask:

Aachen MammoMatrixMasks2.png
Cut Lines
This AcCELLoMatrix mask can be lasercut and placed below a 384-well plate.

Get the DatamatrixMaskDesigner to make you own AcCELLoMatrixes! (requires Windows 7/8)

You can also download the full source code and compile or modify it with Visual Studio (Express) 2013.

For the first experiments, we cut two different data matrix patterns from polypropylen foil. The masks can be used to cover the plates from the top or from the bottom.

Aachen MammoMatrixMasks1.jpg
AcCELLoMatrix masks
These masks can be placed on top or beneath 384-well plates to facilitate localized illumination of wells.

AcCELLoMatrix Reader App

After mask have been designed and the information was encoded into the well plate by selectively illuminating the cells, how do you get it out again? We made an app for that: the AcCELLoMatrix Reader for Windows Phone.

We designed the app to be easy to use: A user can simply open the app

Aachen Collaboration-FRScreenshot1.png
Step 1: Start the app

...read through very brief instructions...

Aachen Collaboration-FRScreenshot2.png
Step 2: Start scanning

...and start scanning for datamatrixes!

170px
Step 3: Aim for datamatrixes in the wild


In the small picture you can see how the frames are pre-processed to be recognized by the ZXing datamatrix recognition algorithm. As soon as the algorithm finds a datamatrix, the string value is decoded and displayed to the user:

170px
Step 4: Displaying the decoded text

Outlook

References

[http://www.nuget.org/packages/ZXing.Net/ ZXing.NET] by Michael Jahn is a port of ZXing ("zebra crossing"), both licensed under [http://www.apache.org/licenses/LICENSE-2.0 Apache 2.0]