Team:ETHZ Basel/Achievements
From 2010.igem.org
Achievements Overview
BioBrick Toolbox
MATLAB Toolbox (Lemming Toolbox)
As a result of our efforts to make all our computer based tools & algorithms modular and re-usable, we have assembled the entire in-silico setup of the E. Lemming into a MATLAB toolbox. This includes the following Simulink modules that encapsulate the algorithms we used.
- Image aquisition - to receive images either from a microscope (live image stream) or to work with saved images in a storage device
- Cell Detection & Tracking - to detect cells in the image streams and keep track of their trajectories through out the image stream
- Microscope control - to adjust the position of the stage to capture the cells properly, to shine red/far-red light on the cells to influence their movement
- Input devices - to capture inputs from a joystick or a keyboard
- Controller - to select a cell & to drive it to a target
- Models (for simulations)
- Molecular Model - capturing & integrating the biological pathways into the simulations
- Movement Model - simulates the motion of the E .lemming
- Image generator - to generate a realistic look & feel for the simulations
- Visualization
- Cell Visualization - outputs the visuals combining the microscope images and the outputs of above Simulink blocks
- E. lemming 2D - the game
The complete toolbox can be downloaded here [add link]. Please visit the MATLAB Toolbox page for further information