Team:ETHZ Basel/InformationProcessing/Visualization

From 2010.igem.org

(Difference between revisions)
(Background)
(User Experience)
 
(20 intermediate revisions not shown)
Line 4: Line 4:
= Visualization and Man-Machine Interface =
= Visualization and Man-Machine Interface =
== Background ==
== Background ==
-
[[Image:userExperience.jpg|thumb|380px|The real-time representation of the current microscope information together with information on all detected cells, the selected cell and its swimming direction, and others. For a description of the single elements in the image, we refer to the text.]]To control the E. lemming, the scientist has to be aware of a huge amount of information, which has to be visualized to him in real-time. Only with this information he or she is able to choose an E. coli cell to control, decide on a reference direction, and interfere in the experiments. This information include
+
<html><div class="thumb tright"><div class="thumbinner" style="width:402px;">
-
* the current microscopy image
+
<iframe title="YouTube video player" class="youtube-player" type="text/html" width="400" height="325" src="http://www.youtube.com/embed/hwtOBgQCAAA?rel=0&hd=1" frameborder="0"></iframe>
-
* all detected, not detected and falsely detected cells
+
<div class="thumbcaption"><div class="magnify"><a href="http://www.youtube.com/watch?v=hwtOBgQCAAA&hd=1" class="external" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>The real-time representation of the current microscope image</b>. <br><i>Blue dots</i>: the detected <i>E. coli</i> cells. <i>Yellow dot</i>: the currently selected E. lemming. <i>Yellow cone</i>: the current swimming direction of E. lemming. <i>Red thin line</i>: the reference direction. <i>Yellow dotted line</i>: the current path of the E. lemming. <br>Note that the movement process is not under the influence of the controller.</br> </div></div></div></html>
-
* the selected cell itself
+
To control E. lemming, the scientist has to be aware of a huge amount of information, which has to be visualized in real-time. Only with this information, the user is able to choose an E. lemming to control, decide on a reference direction, and interfere in the experiments. This information includes
-
* its swimming direction
+
* the current microscopy image;
-
* the reference direction  
+
* all detected, not detected and falsely detected cells;
-
* its path
+
* the selected cell itself;
-
* movements of the stage.
+
* its swimming direction;
 +
* the reference direction;
 +
* its path;
 +
* and movements of the stage.
Since this information has to be absorbed by the experimentalist at a rate higher than three frames per second, a textual representation is not adequate. We thus decided to represent the information in an intuitive way by incorporating it into the microscope images.
Since this information has to be absorbed by the experimentalist at a rate higher than three frames per second, a textual representation is not adequate. We thus decided to represent the information in an intuitive way by incorporating it into the microscope images.
-
<br>
+
 
-
To enable the scientist to interfere with the experiment without having to interrupt it, thus possibly loosing the currently controlled cell, we established two input devices: The user can either control the experiment and the E. lemming using the keyboard or the joystick. With both devices he or she can:
+
To enable the scientist to interfere with the experiment without having to interrupt, and thus possibly losing the currently controlled cell, we established two input devices: the user can either control the experiment and the E. lemming using the keyboard or the joystick. With both devices he/she is able to:
-
* select a cell to control
+
* select a cell to control;
-
* activate or deactivate the controller
+
* activate or deactivate the controller;
-
* set the reference direction
+
* set the reference direction;
-
* increase or decrease the threshold for cell detection (see [Team:ETHZ_Basel/InformationProcessing/CellDetection])
+
* increase or decrease the threshold for cell detection;
-
* alternatively, manually induce red or far-red light pulses of various length (instead of using the controllers provided in the toolbox).  
+
* or, alternatively, manually induce red or far-red light pulses of various length (instead of using the controllers provided in the toolbox).  
If using a force-feedback joystick, the current swimming direction is furthermore given as a small force on the direction of the joystick, thus intuitively increasing the amount of information available for the user.
If using a force-feedback joystick, the current swimming direction is furthermore given as a small force on the direction of the joystick, thus intuitively increasing the amount of information available for the user.
-
Both, the visual representation of the current state of the experiment as well as the user input had to be designed to require low computational efforts to not unnecessarily slow down the imaging.
+
Both, the visual representation of the current state of the experiment as well as the user input had to be designed to require low computational efforts not to unnecessarily slow down the imaging.
== User Experience ==
== 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. All detected cells in the microscope image are highlighted by letting them glow blue (see example picture). The user can select a cell to control with the joystick or the keyboard, which is then glowing yellow instead of blue. The current swimming direction is indicated by a transparent yellow light cone, imitating the floodlight of cars or a flashlight, and the reference direction is depicted as a transparent red line. The path the cell has passed during the experiment is marked by small yellow dots, similar to footprints in snow. Finally, the automatic movement of the stage of the microscope when following a cell which swims out of the current field of view is indicated by arrows in the direction of movement, which are shortly popping up.
+
[[Image:userExperience.jpg|thumb|400px|'''Example Image of the Visualization''']]The images of the microscope are visualized live at a personal computer which is connected to the microscope over a local network or internet, thus it is possible to control the E. lemming from another office or city.  
 +
 
 +
=== Visual Enhancements ===
 +
All detected cells in the microscope image are highlighted by letting them glow blue (see example picture). The user can select a cell to control with the joystick or the keyboard, which is then glowing yellow instead of blue. The current swimming direction is indicated by a transparent yellow light cone, imitating the floodlight of cars or a flashlight, and the reference direction is depicted as a thin red line. The path the cell has passed during the experiment is marked by small yellow dots, similar to footprints in snow. Finally, the automatic movement of the stage of the microscope, when following a cell which swims out of the current field of view, is indicated by arrows in the direction of movement, which are popping up for a moment.

Latest revision as of 01:13, 28 October 2010

Visualization and Man-Machine Interface

Background

The real-time representation of the current microscope image.
Blue dots: the detected E. coli cells. Yellow dot: the currently selected E. lemming. Yellow cone: the current swimming direction of E. lemming. Red thin line: the reference direction. Yellow dotted line: the current path of the E. lemming.
Note that the movement process is not under the influence of the controller.
To control E. lemming, the scientist has to be aware of a huge amount of information, which has to be visualized in real-time. Only with this information, the user is able to choose an E. lemming to control, decide on a reference direction, and interfere in the experiments. This information includes

  • the current microscopy image;
  • all detected, not detected and falsely detected cells;
  • the selected cell itself;
  • its swimming direction;
  • the reference direction;
  • its path;
  • and movements of the stage.

Since this information has to be absorbed by the experimentalist at a rate higher than three frames per second, a textual representation is not adequate. We thus decided to represent the information in an intuitive way by incorporating it into the microscope images.

To enable the scientist to interfere with the experiment without having to interrupt, and thus possibly losing the currently controlled cell, we established two input devices: the user can either control the experiment and the E. lemming using the keyboard or the joystick. With both devices he/she is able to:

  • select a cell to control;
  • activate or deactivate the controller;
  • set the reference direction;
  • increase or decrease the threshold for cell detection;
  • or, alternatively, manually induce red or far-red light pulses of various length (instead of using the controllers provided in the toolbox).

If using a force-feedback joystick, the current swimming direction is furthermore given as a small force on the direction of the joystick, thus intuitively increasing the amount of information available for the user.

Both, the visual representation of the current state of the experiment as well as the user input had to be designed to require low computational efforts not to unnecessarily slow down the imaging.

User Experience

Example Image of the Visualization
The images of the microscope are visualized live at a personal computer which is connected to the microscope over a local network or internet, thus it is possible to control the E. lemming from another office or city.

Visual Enhancements

All detected cells in the microscope image are highlighted by letting them glow blue (see example picture). The user can select a cell to control with the joystick or the keyboard, which is then glowing yellow instead of blue. The current swimming direction is indicated by a transparent yellow light cone, imitating the floodlight of cars or a flashlight, and the reference direction is depicted as a thin red line. The path the cell has passed during the experiment is marked by small yellow dots, similar to footprints in snow. Finally, the automatic movement of the stage of the microscope, when following a cell which swims out of the current field of view, is indicated by arrows in the direction of movement, which are popping up for a moment.