http://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?action=history&feed=atom&title=SectorAnalysisToolbox_DetailsSectorAnalysisToolbox Details - Revision history2026-04-14T20:15:32ZRevision history for this page on the wikiMediaWiki 1.43.8http://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5919&oldid=prevAndrewBangham at 07:52, 19 March 20122012-03-19T07:52:47Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''? Procrustes analysis is used to find the average shape of the organ and each outline together with internal features, the marked sectors, is warped to the average. Then ellipses are fitted to each sector to provide an estimate of growth along the major and minor axes in the region of the sector. The </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''?<ins style="font-weight: bold; text-decoration: none;"></span> </ins>Procrustes analysis is used to find the average shape of the organ and each outline together with internal features, the marked sectors, is warped to the average. Then ellipses are fitted to each sector to provide an estimate of growth along the major and minor axes in the region of the sector. The </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''''' Sector Analysis Toolbox'' is written in [http://en.wikipedia.org/wiki/MATLAB Matlab].''' It does not require any extra Mathworks toolboxes, nor any separately compiled modules. Matlab is available as a [http://www.mathworks.com/products/matlab/tryit.html 30 day free trial] and as a [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]. '' Sector Analysis Toolbox'' comprises around 20,000 lines of code. <br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''''' Sector Analysis Toolbox'' is written in [http://en.wikipedia.org/wiki/MATLAB Matlab].''' It does not require any extra Mathworks toolboxes, nor any separately compiled modules. Matlab is available as a [http://www.mathworks.com/products/matlab/tryit.html 30 day free trial] and as a [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]. '' Sector Analysis Toolbox'' comprises around 20,000 lines of code. <br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''Where'''?</span></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''Where'''?</span></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip <span style="color: Gray">'''''Download''''' </span>]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip <span style="color: Gray">'''''Download''''' </span>]</div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5912&oldid=prevAndrewBangham at 07:52, 19 March 20122012-03-19T07:52:16Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''? <del style="font-weight: bold; text-decoration: none;">What does '' SectorAnalysisToolbox'' require?</span></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''? <ins style="font-weight: bold; text-decoration: none;">Procrustes analysis is used to find the average shape of the organ and each outline together with internal features, the marked sectors, is warped to the average. Then ellipses are fitted to each sector to provide an estimate of growth along the major and minor axes in the region of the sector. The </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''''' Sector Analysis Toolbox'' is written in [http://en.wikipedia.org/wiki/MATLAB Matlab].''' It does not require any extra Mathworks toolboxes, nor any separately compiled modules. Matlab is available as a [http://www.mathworks.com/products/matlab/tryit.html 30 day free trial] and as a [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]. '' Sector Analysis Toolbox'' comprises around 20,000 lines of code. <br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''''' Sector Analysis Toolbox'' is written in [http://en.wikipedia.org/wiki/MATLAB Matlab].''' It does not require any extra Mathworks toolboxes, nor any separately compiled modules. Matlab is available as a [http://www.mathworks.com/products/matlab/tryit.html 30 day free trial] and as a [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]. '' Sector Analysis Toolbox'' comprises around 20,000 lines of code. <br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''Where'''?</span></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''Where'''?</span></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip <span style="color: Gray">'''''Download''''' </span>]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip <span style="color: Gray">'''''Download''''' </span>]</div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5922&oldid=prevAndrewBangham at 07:43, 19 March 20122012-03-19T07:43:23Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|- valign="top"</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|- valign="top"</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|width="700pt"|<span style="color: Navy">'''What'''?</span> We wish to understand how '''patterns of gene activity''' in biological organs influence the developing '''shape'''. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To understand growth it is, therefore, necessary to '''observe and measure growth rates''' throughout the growing organ. Small organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis.<br>Clones of cells arise from divisions of a single cell. Clones become useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, <del style="font-weight: bold; text-decoration: none;">or </del>the '''colour''' of cells in a flower petal. As result of multiple cell divisions, growth, <del style="font-weight: bold; text-decoration: none;">the shape of the clone (sometimes call the sector) </del>can be followed by measuring the shape of the marked clone. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these marked sectors or clones.<br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|width="700pt"|<span style="color: Navy">'''What'''?</span> We wish to understand how '''patterns of gene activity''' in biological organs influence the developing '''shape'''. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To understand growth it is, therefore, necessary to '''observe and measure growth rates''' throughout the growing organ. Small organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis.<br>Clones of cells arise from divisions of a single cell. Clones become useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, the '''colour''' of cells in a flower petal<ins style="font-weight: bold; text-decoration: none;">, or the presence of induced GFP</ins>. As result of multiple cell divisions, growth, can be followed by measuring the shape of the marked clone <ins style="font-weight: bold; text-decoration: none;">(sometimes called sector)</ins>. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these marked sectors or clones.<br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|width="300pt"|[[Image:Sector analysis icon.jpg|180px|SectorAnalysisToolbox]]<br><del style="font-weight: bold; text-decoration: none;">Individual </del>clones observed using confocal microscopy in two regions of an Arabidopsis leaf together with clones (from a number of leaves) that have been identified, labelled and warped <del style="font-weight: bold; text-decoration: none;">to </del>the average leaf shape.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|width="300pt"|[[Image:Sector analysis icon.jpg|180px|SectorAnalysisToolbox]]<br><ins style="font-weight: bold; text-decoration: none;">Left: individual </ins>clones observed using confocal microscopy in two regions of an Arabidopsis leaf together with <ins style="font-weight: bold; text-decoration: none;">(right) the shapes of </ins>clones (from a number of leaves) that have been identified, labelled <ins style="font-weight: bold; text-decoration: none;">(by colour) </ins>and warped <ins style="font-weight: bold; text-decoration: none;">into </ins>the average leaf shape.</div></td></tr>
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</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5923&oldid=prevAndrewBangham at 09:09, 18 March 20122012-03-18T09:09:00Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Software#Analysing the shapes of clones: SectorAnalysisToolbox| Back to BanghamLab software]]<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Software#Analysing the shapes of clones: SectorAnalysisToolbox| Back to BanghamLab software]]<br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=<span style="color: Navy">What? How? Where?</span>=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=<span style="color: Navy">What? How? Where?</span>=</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">[[Image:Sector analysis icon.jpg|256px|SectorAnalysisToolbox]]</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> We wish to understand how '''patterns of gene activity''' in biological organs influence the developing '''shape'''. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To understand growth it is, therefore, necessary to '''observe and measure growth rates''' throughout the growing organ. Small organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">{| border="0" cellpadding="5" cellspacing="3"</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">|- valign="top"</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">|width="700pt"|</ins><span style="color: Navy">'''What'''?</span> We wish to understand how '''patterns of gene activity''' in biological organs influence the developing '''shape'''. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To understand growth it is, therefore, necessary to '''observe and measure growth rates''' throughout the growing organ. Small organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis.<ins style="font-weight: bold; text-decoration: none;"><br>Clones of cells arise from divisions of a single cell. Clones become useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, or the '''colour''' of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) can be followed by measuring the shape of the marked clone. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these marked sectors or clones.<br></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">|width="300pt"|[[Image:Sector analysis icon.jpg|180px|SectorAnalysisToolbox]]<br>Individual clones observed using confocal microscopy in two regions of an Arabidopsis leaf together with clones (from a number of leaves) that have been identified, labelled and warped to the average leaf shape.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">|}</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Clones of cells arise from divisions of a single cell. Clones become useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, or the '''colour''' of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) can be followed by measuring the shape of the marked clone. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these marked sectors or clones.</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''? What does '' SectorAnalysisToolbox'' require?</span></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''? What does '' SectorAnalysisToolbox'' require?</span></div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5918&oldid=prevAndrewBangham at 08:53, 18 March 20122012-03-18T08:53:44Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:53, 18 March 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Software#Analysing the shapes of clones: SectorAnalysisToolbox| Back to BanghamLab software]]<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Software#Analysing the shapes of clones: SectorAnalysisToolbox| Back to BanghamLab software]]<br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=<span style="color: Navy">What? How? Where?</span>=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=<span style="color: Navy">What? How? Where?</span>=</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[Image:<ins style="font-weight: bold; text-decoration: none;">Sector analysis icon</ins>.jpg|256px|<ins style="font-weight: bold; text-decoration: none;">SectorAnalysisToolbox</ins>]]</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[Image:<del style="font-weight: bold; text-decoration: none;">SAT_Main</del>.jpg|256px|<del style="font-weight: bold; text-decoration: none;">thumb|The SAT main application window.</del>]]</div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> We wish to understand how '''patterns of gene activity''' in biological organs influence the developing '''shape'''. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To understand growth it is, therefore, necessary to '''observe and measure growth rates''' throughout the growing organ. Small organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> We wish to understand how '''patterns of gene activity''' in biological organs influence the developing '''shape'''. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To understand growth it is, therefore, necessary to '''observe and measure growth rates''' throughout the growing organ. Small organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis. </div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5921&oldid=prevAndrewBangham at 08:51, 18 March 20122012-03-18T08:51:47Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:51, 18 March 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4">Line 4:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:SAT_Main.jpg|256px|thumb|The SAT main application window.]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:SAT_Main.jpg|256px|thumb|The SAT main application window.]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> We wish to understand how '''patterns of gene activity''' in biological organs influence the developing '''shape'''. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To <del style="font-weight: bold; text-decoration: none;">solve the problem</del>, therefore, <del style="font-weight: bold; text-decoration: none;">it is </del>necessary to '''observe and measure growth rates''' <del style="font-weight: bold; text-decoration: none;">of </del>the growing organ. <del style="font-weight: bold; text-decoration: none;">With small </del>organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> We wish to understand how '''patterns of gene activity''' in biological organs influence the developing '''shape'''. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To <ins style="font-weight: bold; text-decoration: none;">understand growth it is</ins>, therefore, necessary to '''observe and measure growth rates''' <ins style="font-weight: bold; text-decoration: none;">throughout </ins>the growing organ. <ins style="font-weight: bold; text-decoration: none;">Small </ins>organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Clones of cells arise from divisions of a single cell. Clones become useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, or the '''colour''' of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) can be followed by measuring the shape of the marked clone. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these marked sectors or clones.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Clones of cells arise from divisions of a single cell. Clones become useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, or the '''colour''' of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) can be followed by measuring the shape of the marked clone. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these marked sectors or clones.</div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5906&oldid=prevAndrewBangham at 09:01, 16 March 20122012-03-16T09:01:56Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:01, 16 March 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4">Line 4:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:SAT_Main.jpg|256px|thumb|The SAT main application window.]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:SAT_Main.jpg|256px|thumb|The SAT main application window.]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> We wish to understand how patterns of gene activity in biological organs influence the developing shape. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To solve the problem, therefore, it is necessary to observe and measure growth rates of the growing organ. With small organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> We wish to understand how <ins style="font-weight: bold; text-decoration: none;">'''</ins>patterns of gene activity<ins style="font-weight: bold; text-decoration: none;">''' </ins>in biological organs influence the developing <ins style="font-weight: bold; text-decoration: none;">'''</ins>shape<ins style="font-weight: bold; text-decoration: none;">'''</ins>. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To solve the problem, therefore, it is necessary to <ins style="font-weight: bold; text-decoration: none;">'''</ins>observe and measure growth rates<ins style="font-weight: bold; text-decoration: none;">''' </ins>of the growing organ. With small organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Clones of cells arise from divisions of a single cell. <del style="font-weight: bold; text-decoration: none;">It becomes </del>useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, or the colour of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) <del style="font-weight: bold; text-decoration: none;">changes</del>. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these sectors or clones.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Clones of cells arise from divisions of a single cell. <ins style="font-weight: bold; text-decoration: none;">Clones become </ins>useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, or the <ins style="font-weight: bold; text-decoration: none;">'''</ins>colour<ins style="font-weight: bold; text-decoration: none;">''' </ins>of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) <ins style="font-weight: bold; text-decoration: none;">can be followed by measuring the shape of the marked clone</ins>. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these <ins style="font-weight: bold; text-decoration: none;">marked </ins>sectors or clones.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''? What does '' SectorAnalysisToolbox'' require?</span></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''? What does '' SectorAnalysisToolbox'' require?</span></div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5916&oldid=prevAndrewBangham at 08:59, 16 March 20122012-03-16T08:59:08Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:59, 16 March 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Clones of cells arise from divisions of a single cell. It becomes useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, or the colour of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) changes. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these sectors or clones.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Clones of cells arise from divisions of a single cell. It becomes useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, or the colour of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) changes. The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these sectors or clones.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''?</span> <del style="font-weight: bold; text-decoration: none;">The </del>Sector Analysis Toolbox is <del style="font-weight: bold; text-decoration: none;">coded </del>in '''Matlab<del style="font-weight: bold; text-decoration: none;">''' </del>and a <del style="font-weight: bold; text-decoration: none;">valid Matlab licence is required to use it</del>.<del style="font-weight: bold; text-decoration: none;"><br></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''<ins style="font-weight: bold; text-decoration: none;">? What does '' SectorAnalysisToolbox'' require</ins>?</span></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"><span style</del>=<del style="font-weight: bold; text-decoration: none;">"color: Navy"></del>'''<del style="font-weight: bold; text-decoration: none;">Where</del>'<del style="font-weight: bold; text-decoration: none;">''? </del><<del style="font-weight: bold; text-decoration: none;">/span</del>> <del style="font-weight: bold; text-decoration: none;">The toolbox is available for download here. </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">''''' </ins>Sector Analysis Toolbox<ins style="font-weight: bold; text-decoration: none;">'' </ins>is <ins style="font-weight: bold; text-decoration: none;">written </ins>in <ins style="font-weight: bold; text-decoration: none;">[http://en.wikipedia.org/wiki/MATLAB Matlab].</ins>''' <ins style="font-weight: bold; text-decoration: none;">It does not require any extra Mathworks toolboxes, nor any separately compiled modules. </ins>Matlab <ins style="font-weight: bold; text-decoration: none;">is available as a [http://www.mathworks.com/products/matlab/tryit.html 30 day free trial] </ins>and <ins style="font-weight: bold; text-decoration: none;">as </ins>a <ins style="font-weight: bold; text-decoration: none;">[http://www.mathworks</ins>.<ins style="font-weight: bold; text-decoration: none;">com/academia/student_version/?s_cid</ins>=<ins style="font-weight: bold; text-decoration: none;">global_nav student edition]. </ins>'' <ins style="font-weight: bold; text-decoration: none;">Sector Analysis Toolbox</ins>'' <ins style="font-weight: bold; text-decoration: none;">comprises around 20,000 lines of code. <br></ins><<ins style="font-weight: bold; text-decoration: none;">br</ins>></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Requirements</del>: <del style="font-weight: bold; text-decoration: none;">MATLAB</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><span style="color</ins>: <ins style="font-weight: bold; text-decoration: none;">Navy">'''Where'''?</span></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[http://cmpdartsvr1.cmp.uea.ac</ins>.<ins style="font-weight: bold; text-decoration: none;">uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip <span style="color: Gray">'''''Download''''' </span>]</ins></div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5909&oldid=prevAndrewBangham at 08:49, 16 March 20122012-03-16T08:49:50Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:49, 16 March 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:SAT_Main.jpg|256px|thumb|The SAT main application window.]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:SAT_Main.jpg|256px|thumb|The SAT main application window.]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of <del style="font-weight: bold; text-decoration: none;">patches of cells, </del>clones.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> <ins style="font-weight: bold; text-decoration: none;">We wish to understand how patterns of gene activity in biological organs influence the developing shape. The shapes arise because different regions of, for example a sheet of cells, grow at different rates. The problem is that a particular shape outline could arise through a number of different patterns of growth inside the outline. To solve the problem, therefore, it is necessary to observe and measure growth rates of the growing organ. With small organs growth can be tracked at the cell scale using confocal microscopy. As the organ gets larger, this becomes impractical and we use an alternative: clonal analysis. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Clones of cells arise from divisions of a single cell. It becomes useful if the cell (and its daughters) are marked in some way. The mark could be the shape of hairs in a fly wing, or the colour of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) changes. </ins>The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of <ins style="font-weight: bold; text-decoration: none;">these sectors or </ins>clones.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''?</span> The Sector Analysis Toolbox is coded in '''Matlab''' and a valid Matlab licence is required to use it.<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''?</span> The Sector Analysis Toolbox is coded in '''Matlab''' and a valid Matlab licence is required to use it.<br></div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&diff=5911&oldid=prevAndrewBangham at 08:20, 16 March 20122012-03-16T08:20:24Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:20, 16 March 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth by analysing the shapes of patches of cells, clones.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''What'''?</span> The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth<ins style="font-weight: bold; text-decoration: none;">''' </ins>by analysing the shapes of patches of cells, clones.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''?</span> The Sector Analysis Toolbox is coded in '''Matlab''' and a valid Matlab licence is required to use it.<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span style="color: Navy">'''How'''?</span> The Sector Analysis Toolbox is coded in '''Matlab''' and a valid Matlab licence is required to use it.<br></div></td></tr>
</table>AndrewBangham