"
Team:Virginia/Software
From 2013.igem.org
(Created page with "<!--DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"--> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <...") |
|||
| (3 intermediate revisions not shown) | |||
| Line 222: | Line 222: | ||
margin-left:auto; | margin-left:auto; | ||
clear:both; | clear:both; | ||
| + | } | ||
| + | #groupbio a { | ||
| + | text-decoration:none; | ||
| + | color:#66ccff; | ||
} | } | ||
| Line 286: | Line 290: | ||
<p>clc3jz@virginia.edu</p> | <p>clc3jz@virginia.edu</p> | ||
<p> if you would like files immediately or any further information. </p> | <p> if you would like files immediately or any further information. </p> | ||
| - | + | <br> | |
<a href="http://www.mathworks.com/matlabcentral/fileexchange/authors/397273">UVa iGem Math Works Profile </a> | <a href="http://www.mathworks.com/matlabcentral/fileexchange/authors/397273">UVa iGem Math Works Profile </a> | ||
| - | <br><br> | + | <br><br><br> |
| - | <p>Program Summary: We recognize our optimal IPTG induction levels may not be the same across different strains or different bacteria. We hope our program will save future users time optimizing IPTG minicell induction levels. With this program, users can save time by avoiding purification before counting. In addition, sorting algorithms | + | <p>Program Summary: We recognize our optimal IPTG induction levels may not be the same across different strains or different bacteria. We hope our program will save future users time optimizing IPTG minicell induction levels. With this program, users can save time by avoiding purification before counting. In addition, sorting algorithms allow users to process many images at the same time. </p> |
<p>Our program processes purified or unpurified images of minicells and returns minicell counts and population statistics. </p> | <p>Our program processes purified or unpurified images of minicells and returns minicell counts and population statistics. </p> | ||
<img src="https://static.igem.org/mediawiki/2013/thumb/6/64/Countme.png/800px-Countme.png" width="800"> | <img src="https://static.igem.org/mediawiki/2013/thumb/6/64/Countme.png/800px-Countme.png" width="800"> | ||
| Line 301: | Line 305: | ||
<li>Plots cells in image on various bar graphs and histograms </li> | <li>Plots cells in image on various bar graphs and histograms </li> | ||
</p> | </p> | ||
| - | + | <img src="https://static.igem.org/mediawiki/2013/b/ba/Softwarecellcounts.png" width="800"> | |
</div> | </div> | ||
Latest revision as of 02:58, 29 October 2013
We hope to keep improving our code as we continue to research our minicells after the International Jamboree. To access the most recent versions, please check out our MatLab File Exchange page, available below. Files may take up to a week to be approved, so feel free to contact
Chris Cai
clc3jz@virginia.edu
if you would like files immediately or any further information.
UVa iGem Math Works Profile
Program Summary: We recognize our optimal IPTG induction levels may not be the same across different strains or different bacteria. We hope our program will save future users time optimizing IPTG minicell induction levels. With this program, users can save time by avoiding purification before counting. In addition, sorting algorithms allow users to process many images at the same time.
Our program processes purified or unpurified images of minicells and returns minicell counts and population statistics.
Functionality
- Converts fluorescent images to binary matrixes
- Removes glare from images by generating a ‘disc’ structural element
- Removes insignificant particles based on area thresholding algorithms or by manual input.
- Counts total number of cells
- Uses Support Vector Machine algorithms to classify cells as minicells or parent cell (requires “calibration cases” to “train” the machine)
- Plots cells in image on various bar graphs and histograms
