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

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===[[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection/Video1|Video1]]===
===[[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection/Video1|Video1]]===
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===Video 2===
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===[[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection/Video2|Video2]]===
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This video was recorded with higher contrast and with a better focus than for Video1. The video was shot at 12 fps for a duration of 1 min. The cells and their wall can clearly be seen over all frames. Note that the inside of the wall is darker than the cell membrane.
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[[Image:Video_2.gif|400px]]
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Notice (see below) the presence of some noisy circular patterns. These patterns are found at fixed positions over all frames.
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[[Image:Noise2r.tiff]]
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Intensity properties for the background, cells and noisy circular patterns can be found below. As well as shape characteristics for the cells.
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[http://openwetware.org/wiki/Image:Background2.xls Background]
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[http://openwetware.org/wiki/Image:Cells2.xls Cells]
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[http://openwetware.org/wiki/Image:Pattern2.xls Circular Patterns]
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=Manual Tracking Methodology=
=Manual Tracking Methodology=

Revision as of 12:26, 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. 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 ???)

Video1

Video2

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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