Team:Valencia Biocampus/Devices

iGEM Scanner

iGEM Scanner was created entirely with LEGO, and will be able to detect and create an image of the concentration of various substrates in order to be analysed afterwards and facilitate the work in modeling.

It seems unbelievable that you can do that, but LEGO is no more only for children: there is a new LEGO tool called LEGO Mindstorms that allows users to bring to life their own constructions, by programming it in an integrated development environment.

Automatons designed this way, are based in two actions: they can obtain different type of measurements from their surrounding by sensing it, and also perform some work with its engines. The sensors that can be used are: sound, colour, proximity, touch, temperature and light sensor. This last one was used to carry out the main function of our machine.

Light sensors are composed of a photodiode, an electronic component that can work in two states: photovoltaic mode, when the voltage supplied is zero, its current and voltage in terminals don't vary much with the light intensity; and photoconductive mode, when the voltage supplied is positive, its current is very sensitive to the light intensity. This last state is the most interesting, and the one used in our machine.

LEGO Mindstorms allows you to program a set of measurements done by this sensor spread steadily over time (in our case, less than one-hundredth of a second between two equispaced mesurements). Each one of this data will be transformed in a single pixel of the final image. Also, to permit the sensor move around all the image (to be scanned), we implemented two motors, in order to obtain the two degrees of movement needed for 2D.

C++Elegans

C++Elegans is a lightweight and easy to use image manipulation and analysis software written in C++. It is cross-platform in part due to the use of the open-source GUI library [http://www.wxwidgets.org wxWidgets]. This means it can be compiled and run in several different Operating Systems, such as Linux, Windows and Mac OSX. It is also open-source which means all the code will be freely available and modifiable under the [http://www.gnu.org/licenses/gpl.html GPL v3.0 License].
C++Elegans is being written as part of our iGEM project and makes use of some usual image analysis algorithms.

Downloads

Screenshots

Usage

C++Elegans is very easy to use thanks to the descriptive menus and the simple graphical user interface. The menu is divided into different categories: File, View, Edit and Help. Each of these menus are subdivided into different sub-menus. The status bar gives information about the tools, the current state of C++Elegans, the zoom factor and the local data & time. The menu bar hierarchy (explained) is as follows:

• File
  • Open → Open and load an image, supported formats are: .bmp, .gif, .png, .jpeg, .jpg, .tga, .tiff, .iff, .pcx, .pnm, .xpm, .ico, .ani and .cur.
  • Save → Save current image with the same filename (overwrite), supported formats are: .bmp, .png, .jpg, .tga and .tiff.
  • Save As → Save current image with a new filename, supported formats are: .bmp, .png, .jpg, .tga and .tiff.
  • Quit → Simply quits C++Elegans, it will remind you of changes made to the image that were not saved.
• View
  • Zoom Reset → Reset the zoom (Set zoom factor to 100%).
  • Zoom In → Increment the zoom factor.
  • Zoom Out → Decrement the zoom factor.
  • Status Bar → Toggle status bar visibility.
  • Toolbar → Toggle toolbar visibility.
• Edit
  • Colour
    • Invert colours → Inverts the colours of the image. Negative image.
    • Convert to greyscale → Converts the image to greyscale colours.
    • Brightness & Contrast → Allows to change the brightness and the contrast of the image by means of two sliders.
    • Hue, Saturation & Value → Allows to adjust the hue, saturation and value of the image.
    • Automatically adjust value → As its name describes auto-adjusts the value of the image by means of a simple algorithm.
    • Automatically adjust colours → As its name describes auto-adjusts the colours of the image by means of a simple algorithm.
    • Automatically adjust levels → As its name describes auto-adjusts the levels of the image by means of a simple algorithm.
  • Filters → Shows the filters dialog, which allows to apply several different filters to the image with a specific size and as many times as the iterations field indicates. As of now the available filters are:
    1. Median
    2. Mean
    3. Midpoint
    4. Gaussian
  • Edge detection
    • Gaussian → shows simple gaussian edge detection dialog.
• Help
  • Help → Redirects to this webpage for the moment.
  • About → Information about C++Elegans, version, credits, license, etc.

Note that Undo & Redo actions are not implemented as of yet and may not be implemented in the near future, so it is recommended that one saves the image (Save As [Ctrl+W]) with a different name after each substantial change.

License

As mentioned above, C++Elegans and its complete source code is freely available under the GPL license, which can be found here:
[http://www.gnu.org/licenses/gpl.html GPL v3.0 License]