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Team:ETHZ Basel/InformationProcessing/Visualization
From 2010.igem.org
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= Visualization = | = Visualization = | ||
| + | == User Experience == | ||
| + | The images of the microscope are visualized live at a personal computer which is connected to the microscope over a local network or the internet, thus it is possible to control the E. lemming from another office or city. To enhance the user experience, all detected cells in the microscope image are highlighted by letting them glow blue (see example movie below). The user can select a cell with the joystick, which is then highlighted by a yellow glowing to simplify the tracking. Furthermore, the current direction of the cell is visualized by a semi-transparent yellow light cone and the path the cell has already travelled is marked by yellow dots. | ||
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| + | The user can select a direction with the joystick he wants the E. lemming to go, which is visualized by a red line. The controller (see [Team:ETHZ_Basel/Modeling/Controller Controller]) then automatically tries, by sending red and far-red light signals, to force the E. lemming in this direction. Alternatively the user can send the light signals on his own by using the buttons of the joystick. | ||
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| + | If the cell moves out of the current image of the microscope, this is detected by the controller and the microscope is automatically moved so that the cell is always in the central 50% of the image. The user furthermore can change during the simulation the threshold of the cell detection algorithm (see [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/CellDetection Cell Detection]) to detect either more cells (but also possibly more false positive ones) or less cells (which may reduce the number of true positives). | ||
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| + | == Example Movie == | ||
<html> | <html> | ||
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Revision as of 12:35, 16 September 2010
Visualization
User Experience
The images of the microscope are visualized live at a personal computer which is connected to the microscope over a local network or the internet, thus it is possible to control the E. lemming from another office or city. To enhance the user experience, all detected cells in the microscope image are highlighted by letting them glow blue (see example movie below). The user can select a cell with the joystick, which is then highlighted by a yellow glowing to simplify the tracking. Furthermore, the current direction of the cell is visualized by a semi-transparent yellow light cone and the path the cell has already travelled is marked by yellow dots.
The user can select a direction with the joystick he wants the E. lemming to go, which is visualized by a red line. The controller (see [Team:ETHZ_Basel/Modeling/Controller Controller]) then automatically tries, by sending red and far-red light signals, to force the E. lemming in this direction. Alternatively the user can send the light signals on his own by using the buttons of the joystick.
If the cell moves out of the current image of the microscope, this is detected by the controller and the microscope is automatically moved so that the cell is always in the central 50% of the image. The user furthermore can change during the simulation the threshold of the cell detection algorithm (see Cell Detection) to detect either more cells (but also possibly more false positive ones) or less cells (which may reduce the number of true positives).
Example Movie
The cells were placed in a 50 μm (?) high flow chamber (Details). The excitation for the bright field images (40x) was 60ms, the period something around 0.3s, aproximately corresponding to the fps rate of the movie. To increase speed, the binning in the microscope was set to 2, so that the images were 672 x 512 grayscale (16 bit) instead of the maximal resolution of the microscope of 1344 x 1024 pixels, and every pixel The images were made out-of-focus to simplify cell detection.
