SectorAnalysisToolbox Details: Difference between revisions
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[[Software#Analysing the shapes of clones: SectorAnalysisToolbox| Back to BanghamLab software]]<br> | |||
=<span style="color: Navy">What? How? Where?</span>= | =<span style="color: Navy">What? How? Where?</span>= | ||
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|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, or the presence of induced GFP. As result of multiple cell divisions, growth, can be followed by measuring the shape of the marked clone (sometimes called sector). The Sector Analysis Toolbox '''(SAT)''' is used ''' to quantify patterns of growth''' by analysing the shapes of these marked sectors or clones.<br> | |||
|width="300pt"|[[Image:Sector analysis icon.jpg|180px|SectorAnalysisToolbox]]<br>Left: individual clones observed using confocal microscopy in two regions of an Arabidopsis leaf together with (right) the shapes of clones (from a number of leaves) that have been identified, labelled (by colour) and warped into the average leaf shape. | |||
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<span style="color: Navy"> | <span style="color: Navy">'''How'''?</span> 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 | ||
''''' 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> | |||
<span style="color: Navy">'''Where'''?</span> | |||
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip <span style="color: Gray">'''''Download''''' </span>] | |||
<span style="color: Navy">''' | |||
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Latest revision as of 07:52, 19 March 2012
What? How? Where?
| What? 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. 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, or the presence of induced GFP. As result of multiple cell divisions, growth, can be followed by measuring the shape of the marked clone (sometimes called sector). The Sector Analysis Toolbox (SAT) is used to quantify patterns of growth by analysing the shapes of these marked sectors or clones. |
 Left: individual clones observed using confocal microscopy in two regions of an Arabidopsis leaf together with (right) the shapes of clones (from a number of leaves) that have been identified, labelled (by colour) and warped into the average leaf shape. |
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
Sector Analysis Toolbox is written in Matlab. It does not require any extra Mathworks toolboxes, nor any separately compiled modules. Matlab is available as a 30 day free trial and as a student edition. Sector Analysis Toolbox comprises around 20,000 lines of code.
Where? Download