IGEM:IMPERIAL/2008/Prototype/Drylab/Motility data collection: Difference between revisions

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=Data Clustering=
=Data Clustering=
*By plotting velocity*exp(i*angle) in the complex plane for each frame, we hope to be able to segment our data into two clusters:
**One defining the tumble phase
**One defining the run phase
*This segmentation would then be used by our analysis program to derive the following properties: run time, tumble time, run velocity, tumble angle.


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Revision as of 11:29, 5 September 2008

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<html><a href=http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype><img width=50px src=http://openwetware.org/images/f/f2/Imperial_2008_Logo.png></img</a></html> Home The Project B.subtilis Chassis Wet Lab Dry Lab Notebook

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Our Approach

Material

We will be using the Zeiss Axiovert 200 inverted microscope with a fully motorised stage, controlled by Improvision Volocity acquisition software. This system offers a full incubation chamber with temperature and CO2 control, a large range of filter sets from UV to far-red and a highly sensitive 1300x1000 pixel camera for fast low-light imaging.

Video images are captured into memory by the system at a basal video frame rate of 16.3Hz. This can be further increased by performing binning.


Microscope Video Characteristics

  • From our experience on the microscope, we observe the following:
    • Bacteria are rod shaped.
    • Some cells swim out of the focus plane
    • The images are noisy
    • Some cells seem to be undergoing division
    • Some cells appear to be dead as they are not moving or drift


Video1

Video2

Video3

Manual Tracking Methodology

  • We intend to track for each cell:
    • The centroid
    • The part of the cell in the direction of movement
  • We attempt to reduce the bias in our manual tracking
    • By disabling the view path option
    • By displacing the cursor away from the tracked cell before adding a new point

Data Clustering

  • By plotting velocity*exp(i*angle) in the complex plane for each frame, we hope to be able to segment our data into two clusters:
    • One defining the tumble phase
    • One defining the run phase
  • This segmentation would then be used by our analysis program to derive the following properties: run time, tumble time, run velocity, tumble angle.



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