http://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=SectorAnalysisToolbox_Details&feed=atom&action=historySectorAnalysisToolbox Details - Revision history2024-03-29T08:53:10ZRevision history for this page on the wikiMediaWiki 1.35.5http://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;"></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;"></td></tr>
<tr><td class='diff-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'>+</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 class="diffchange diffchange-inline"></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;"></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;"></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;"></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;"></td></tr>
<tr><td class='diff-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 class="diffchange diffchange-inline">What does '' SectorAnalysisToolbox'' require?</span></del></div></td><td class='diff-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 class="diffchange diffchange-inline">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;"></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;"></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>{| border="0" cellpadding="5" cellspacing="3"</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>{| border="0" cellpadding="5" cellspacing="3"</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>|- 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'>−</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 class="diffchange diffchange-inline">or </del>the '''colour''' of cells in a flower petal. As result of multiple cell divisions, growth, <del class="diffchange diffchange-inline">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'>+</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 class="diffchange diffchange-inline">, 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 class="diffchange diffchange-inline">(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'>−</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 class="diffchange diffchange-inline">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 class="diffchange diffchange-inline">to </del>the average leaf shape.</div></td><td class='diff-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 class="diffchange diffchange-inline">Left: individual </ins>clones observed using confocal microscopy in two regions of an Arabidopsis leaf together with <ins class="diffchange diffchange-inline">(right) the shapes of </ins>clones (from a number of leaves) that have been identified, labelled <ins class="diffchange diffchange-inline">(by colour) </ins>and warped <ins class="diffchange diffchange-inline">into </ins>the average leaf shape.</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>|}</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>|}</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><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</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'>−</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"> </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;"></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;"></td></tr>
<tr><td class='diff-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'>+</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 class="diffchange diffchange-inline">{| border="0" cellpadding="5" cellspacing="3"</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-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 class="diffchange diffchange-inline">|- valign="top"</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-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 class="diffchange diffchange-inline">|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 class="diffchange diffchange-inline"><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"> </td><td class='diff-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 class="diffchange diffchange-inline">|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"> </td><td class='diff-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 class="diffchange diffchange-inline">|}</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;"></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;"></td></tr>
<tr><td class='diff-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"> </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;"></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;"></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>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 08:53, 18 March 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</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>[[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'>−</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'>+</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 class="diffchange diffchange-inline">Sector analysis icon</ins>.jpg|256px|<ins class="diffchange diffchange-inline">SectorAnalysisToolbox</ins>]]</div></td></tr>
<tr><td class='diff-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 class="diffchange diffchange-inline">SAT_Main</del>.jpg|256px|<del class="diffchange diffchange-inline">thumb|The SAT main application window.</del>]]</div></td><td colspan="2"> </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;"></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;"></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 class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<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 08:51, 18 March 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td>
<td colspan="2" class="diff-lineno">Line 4:</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>[[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;"></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;"></td></tr>
<tr><td class='diff-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 class="diffchange diffchange-inline">solve the problem</del>, therefore, <del class="diffchange diffchange-inline">it is </del>necessary to '''observe and measure growth rates''' <del class="diffchange diffchange-inline">of </del>the growing organ. <del class="diffchange diffchange-inline">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'>+</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 class="diffchange diffchange-inline">understand growth it is</ins>, therefore, necessary to '''observe and measure growth rates''' <ins class="diffchange diffchange-inline">throughout </ins>the growing organ. <ins class="diffchange diffchange-inline">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;"></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;"></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 class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<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 09:01, 16 March 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td>
<td colspan="2" class="diff-lineno">Line 4:</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>[[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;"></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;"></td></tr>
<tr><td class='diff-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'>+</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 class="diffchange diffchange-inline">'''</ins>patterns of gene activity<ins class="diffchange diffchange-inline">''' </ins>in biological organs influence the developing <ins class="diffchange diffchange-inline">'''</ins>shape<ins class="diffchange diffchange-inline">'''</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 class="diffchange diffchange-inline">'''</ins>observe and measure growth rates<ins class="diffchange diffchange-inline">''' </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;"></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;"></td></tr>
<tr><td class='diff-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 class="diffchange diffchange-inline">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 class="diffchange diffchange-inline">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'>+</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 class="diffchange diffchange-inline">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 class="diffchange diffchange-inline">'''</ins>colour<ins class="diffchange diffchange-inline">''' </ins>of cells in a flower petal. As result of multiple cell divisions, growth, the shape of the clone (sometimes call the sector) <ins class="diffchange diffchange-inline">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 class="diffchange diffchange-inline">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;"></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;"></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 class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<col class="diff-content" />
<tr class="diff-title" lang="en">
<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 08:59, 16 March 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l8" >Line 8:</td>
<td colspan="2" class="diff-lineno">Line 8:</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. 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;"></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;"></td></tr>
<tr><td class='diff-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 class="diffchange diffchange-inline">The </del>Sector Analysis Toolbox is <del class="diffchange diffchange-inline">coded </del>in '''Matlab<del class="diffchange diffchange-inline">''' </del>and a <del class="diffchange diffchange-inline">valid Matlab licence is required to use it</del>.<del class="diffchange diffchange-inline"><br></del></div></td><td class='diff-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 class="diffchange diffchange-inline">? What does '' SectorAnalysisToolbox'' require</ins>?</span></div></td></tr>
<tr><td class='diff-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 class="diffchange diffchange-inline"><span style</del>=<del class="diffchange diffchange-inline">"color: Navy"></del>'''<del class="diffchange diffchange-inline">Where</del>'<del class="diffchange diffchange-inline">''? </del><<del class="diffchange diffchange-inline">/span</del>> <del class="diffchange diffchange-inline">The toolbox is available for download here. </del></div></td><td class='diff-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 class="diffchange diffchange-inline">''''' </ins>Sector Analysis Toolbox<ins class="diffchange diffchange-inline">'' </ins>is <ins class="diffchange diffchange-inline">written </ins>in <ins class="diffchange diffchange-inline">[http://en.wikipedia.org/wiki/MATLAB Matlab].</ins>''' <ins class="diffchange diffchange-inline">It does not require any extra Mathworks toolboxes, nor any separately compiled modules. </ins>Matlab <ins class="diffchange diffchange-inline">is available as a [http://www.mathworks.com/products/matlab/tryit.html 30 day free trial] </ins>and <ins class="diffchange diffchange-inline">as </ins>a <ins class="diffchange diffchange-inline">[http://www.mathworks</ins>.<ins class="diffchange diffchange-inline">com/academia/student_version/?s_cid</ins>=<ins class="diffchange diffchange-inline">global_nav student edition]. </ins>'' <ins class="diffchange diffchange-inline">Sector Analysis Toolbox</ins>'' <ins class="diffchange diffchange-inline">comprises around 20,000 lines of code. <br></ins><<ins class="diffchange diffchange-inline">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;"></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;"></td></tr>
<tr><td class='diff-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 class="diffchange diffchange-inline">Requirements</del>: <del class="diffchange diffchange-inline">MATLAB</del>.</div></td><td class='diff-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 class="diffchange diffchange-inline"><span style="color</ins>: <ins class="diffchange diffchange-inline">Navy">'''Where'''?</span></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-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 class="diffchange diffchange-inline">[http://cmpdartsvr1.cmp.uea.ac</ins>.<ins class="diffchange diffchange-inline">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>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<col class="diff-content" />
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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 08:49, 16 March 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td>
<td colspan="2" class="diff-lineno">Line 4:</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>[[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;"></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;"></td></tr>
<tr><td class='diff-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 class="diffchange diffchange-inline">patches of cells, </del>clones.</div></td><td class='diff-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 class="diffchange diffchange-inline">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"> </td><td class='diff-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"> </td><td class='diff-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 class="diffchange diffchange-inline">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 class="diffchange diffchange-inline">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;"></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;"></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>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<tr class="diff-title" lang="en">
<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 08:20, 16 March 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td>
<td colspan="2" class="diff-lineno">Line 4:</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>[[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;"></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;"></td></tr>
<tr><td class='diff-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'>+</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 class="diffchange diffchange-inline">''' </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;"></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;"></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