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software_staqtool [2016/10/07 18:06]
bioimaging
software_staqtool [2018/04/03 17:14]
bioimaging
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 +**STaQTool** was developed for automated tracking of a transcription site in the cell nucleus, measuring its fluorescence intensity by Gaussian fitting and analyzing patterns of changes in fluorescence intensity over time. STaQTool runs in any PC with MATLAB Compiler Runtime. The software is a set of open-source MATLAB functions integrated into a single GUI which integrates all functions in a self-explanatory interface and allows for data visualization and easy adjustment of tracking and fitting parameters, as well as automated calibration procedures and analysis of either single transcription sites or multiple mRNA particles moving throughout the nucleus or the cytoplasm. Results such as coordinates of the transcription site and total fluorescence intensity (TFI) are saved to Excel files automatically and allow the user to pause and resume analysis at any time, as well as set up batch analysis of multiple files for unattended automated processing.
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 <img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=staqtool_about.png"​ width=450>​ </td> <img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=staqtool_about.png"​ width=450>​ </td>
-<td style="​border:​0px solid white; vertical-align:​top">​ <br> <h3> &rarr; <a href="https://dl.dropboxusercontent.com/u/7689116/​Bioimaging/​STaQTool_setup.zip"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=download-btn.png"​ width=120>​ setup file for Windows x64 [11.00 Mb]</​a>​ </h3> (installs <a href="​http://​www.mathworks.com/​products/​compiler/​mcr/">​MATLAB Compiler Runtime 9.0.1</​a>​ if not present) ​ &nbsp; <BR> <BR> <h3> &rarr; <a href="https://dl.dropboxusercontent.com/u/7689116/​Bioimaging/​STaQTool_code.zip"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=download-btn.png"​ width=120>​ MATLAB code [1.50 Mb]</​a>​ </h3> (for <a href="​http://​www.mathworks.com/​products/​matlab/">​MATLAB 2016a</​a>,​ may not work in versions earlier than 2015a) </h3> <BR> <BR> <​BR> ​<​BR>  ​<h4> First used in: <a href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​24035393">​Martin et al. Cell Rep. (2013) 4(6):​1144-55</​a>​ </h4> <BR> <h4> Please cite: <a href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​26855377">​Rino et al. Methods (2016) 4(6) 98:​143-9</​a>​ </​h4> ​+<td style="​border:​0px solid white; vertical-align:​top">​ <br> <h3> &rarr; <a href="/​facility/bioimaging/lib/exe/fetch.php?​media=STaQTool_setup.zip"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=download-btn.png"​ width=120>​ setup file for Windows x64 [11.00 Mb]</​a>​ </h3> (installs <a href="​http://​www.mathworks.com/​products/​compiler/​mcr/">​MATLAB Compiler Runtime 9.0.1</​a>​ if not present) ​ &nbsp; <BR> <BR> <h3> &rarr; <a href="/​facility/bioimaging/lib/exe/fetch.php?​media=STaQTool_code.zip"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=download-btn.png"​ width=120>​ MATLAB code [1.50 Mb]</​a>​ </h3> (for <a href="​http://​www.mathworks.com/​products/​matlab/">​MATLAB 2016a</​a>,​ may not work in versions earlier than 2015a) </h3> <BR> <BR> <BR> <h4> First used in: <a href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​24035393">​Martin et al. Cell Rep. (2013) 4(6):​1144-55</​a>​ </h4> <BR> 
 +<h4> Detailed instructions:​ <a href="​https://​www.ncbi.nlm.nih.gov/​pubmed/​28324612">​Rino et al. Methods Mol Biol (2016)</​a>​ <br> <​h5>​(check Video S1 for step by step demonstration)</​h5>​ </h4> <​BR>​ 
 +<h4> Please cite: <a href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​26855377">​Rino et al. Methods (2016) 4(6) 98:​143-9</​a>​ </​h4> ​
 <BR> <BR> <BR> <BR> <​h4>​Change Log</​h4>​ <BR> <BR> <BR> <BR> <​h4>​Change Log</​h4>​
 1.1.1 - fix for non-english versions of Excel <BR> 1.1.1 - fix for non-english versions of Excel <BR>
software_staqtool.txt · Last modified: 2018/04/03 17:15 by bioimaging