IGEM:IMPERIAL/2008/Prototype/Drylab/Motility data collection: Difference between revisions
| Line 31: | Line 31: | ||
[http://openwetware.org/wiki/Image:Pattern1.xls Circular Patterns] | [http://openwetware.org/wiki/Image:Pattern1.xls Circular Patterns] | ||
==Video 2== | ===Video 2=== | ||
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. | 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. | ||
Revision as of 08:06, 4 September 2008
<html> <style type="text/css"> .firstHeading {display: none;} </style> </html> <html> <style type="text/css">
table.calendar { margin:0; padding:2px; }
table.calendar td { margin:0; padding:1px; vertical-align:top; } table.month .heading td { padding:1px; background-color:#FFFFFF; text-align:center; font-size:120%; font-weight:bold; } table.month .dow td { text-align:center; font-size:110%; } table.month td.today { background-color:#3366FF } table.month td {
border:2px; margin:0; padding:0pt 1.5pt; font-size:8pt; text-align:right; background-color:#FFFFFF; }
- bodyContent table.month a { background:none; padding:0 }
.day-active { font-weight:bold; } .day-empty { color:black; } </style> </html>
| <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 |
|---|
<html> <style type="text/css"> div.Section { font:11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; }
/* Text (paragraphs) */ div.Section p { font:11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align:justify; margin-top:0px; margin-left:30px; margin-right:30px; }
/* Headings */ div.Section h1 { font:22pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align:left; color:#3366FF; }
/* Subheadings */ div.Section h2 { font:18pt Calibri, Verdana, Arial, Geneva, sans-serif; color:#3366FF; margin-left:5px; }
/* Subsubheadings */ div.Section h3 { font:16pt Calibri, Verdana, Arial, sans-serif; font-weight:bold; color:#3366FF; margin-left:10px; }
/* Subsubsubheadings */ div.Section h4 { font:12pt Calibri, Verdana, Arial, sans-serif; color:#3366FF; margin-left:15px; }
/* Subsubsubsubheadings */ div.Section h5 { font:12pt Calibri, Verdana, Arial, sans-serif; color:#3366FF; margin-left:20px; }
/* References */ div.Section h6 { font:12pt Calibri, Verdana, Arial, sans-serif; font-weight:bold; font-style:italic; color:#3366FF; margin-left:25px; }
/* Hyperlinks */ div.Section a {
}
div.Section a:hover {
}
/* Tables */ div.Section td { font:11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align:justify; vertical-align:top; padding:2px 4px 2px 4px; }
/* Lists */ div.Section li { font:11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align:left; margin-top:0px; margin-left:30px; margin-right:0px; }
/* TOC stuff */ table.toc { margin-left:10px; }
table.toc li { font: 11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align: justify; margin-top: 0px; margin-left:2px; margin-right:2px; }
/* [edit] links */ span.editsection { color:#BBBBBB; font-size:10pt; font-weight:normal; font-style:normal; vertical-align:bottom; } span.editsection a { color:#BBBBBB; font-size:10pt; font-weight:normal; font-style:normal; vertical-align:bottom; } span.editsection a:hover { color:#3366FF; font-size:10pt; font-weight:normal; font-style:normal; vertical-align:bottom; }
- sddm {
margin: 0; padding: 0; z-index: 30 }
- sddm li {
margin: 0; padding: 0; list-style: none; float: center; font: bold 12pt Calibri, Verdana, Arial, Geneva, sans-serif; border: 0px }
- sddm li a {
display: block; margin: 0px 0px 0px 0px; padding: 0 0 12px 0; background: #33bbff; color: #FFFFFF; text-align: center; text-decoration: none; }
- sddm li a:hover {
border: 0px }
- sddm div {
position: absolute; visibility: hidden; margin: 0; padding: 0; background: #33bbff; border: 1px solid #33bbff } #sddm div a { position: relative; display: block; margin: 0; padding: 5px 10px; width: auto; white-space: nowrap; text-align: left; text-decoration: none; background: #FFFFFF; color: #2875DE; font: 11pt Calibri, Verdana, Arial, Geneva, sans-serif } #sddm div a:hover { background: #33bbff; color: #FFFFFF } </style></html>
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 ???)
Video 1
Our first video.The cells are out of focus.
Notice (see below) the presence of some noisy circular patterns. These patterns are found at fixed positions over all frames.
Intensity properties for the background, cells and noisy circular patterns can be found below. As well as shape characteristics for the cells.
Background Cells Circular Patterns
Video 2
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.
Notice (see below) the presence of some noisy circular patterns. These patterns are found at fixed positions over all frames.
Intensity properties for the background, cells and noisy circular patterns can be found below. As well as shape characteristics for the cells.
Background Cells Circular Patterns
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
<html><center><table style="color:#ffffff;background-color:#66aadd;" cellpadding="3" cellspacing="1" border="0" bordercolor="#ffffff" align="center">
<tr><td><ul id="sddm"></html>[[IGEM:IMPERIAL/2008/New/{{{1}}}|< Previous]]<html></ul>
</td><td><ul id="sddm"><a href="#">Back to top</a></ul>
</td><td><ul id="sddm"></html>[[IGEM:IMPERIAL/2008/New/{{{2}}}|Next >]]<html></ul>
</td></tr></table>
</center></html>
