IGEM:IMPERIAL/2008/Prototype/Drylab/Motility data collection
m (→Microscope Video Characteristics)
m (→Data Clustering)
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Revision as of 13:29, 5 September 2008
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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
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
- 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.