IGEM:IMPERIAL/2008/Prototype/Drylab/Motility data collection

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=Microscope Video Characteristics=
=Microscope Video Characteristics=
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From our experience on the microscope, we observe the following:
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*From our experience on the microscope, we observe the following:
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**Bacteria are rod shaped.
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**Some cells swim out of the focus plane
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**The images are noisy
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**Some cells seem to be undergoing division
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Bacteria are rod shaped. As the bacteria transverse across the plate, it may change shape and orientation. Due to tumbling in the z-direction, bacteria may go in and out of focus. This leads to change in light intensity. Background noise is also present. We also observe a few static noisy spots over all images ( might be due to dust particles ???)
 
===[[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection/Video1|Video1]]===
===[[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection/Video1|Video1]]===
===[[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection/Video2|Video2]]===
===[[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection/Video2|Video2]]===
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===[[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection/Video3|Video3]]===
=Manual Tracking Methodology=
=Manual Tracking Methodology=

Revision as of 13:35, 5 September 2008

Home The Project B.subtilis Chassis Wet Lab Dry Lab Notebook


Contents

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


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


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