SectorAnalysisToolbox Documentation
The models shown in these tutorials illustrate features of the SectorAnalysisToolbox software. Viewing these pages. Some versions of Firefox and Explorer do not create satisfactory prints even though you can view the pages with no problems. Chrome does appear to produce good printouts.
Using the SectorAnalysisToolbox ' to analyse the shapes of cell clones'
How to use the tutorial. First download and install the SectorAnalysisToolbox . A zip file containing the project (Leaf growth) should be loaded. Then, from Matlab, change directory into the project and launch the SectorAnalysisToolbox
1 Creating a new project
To create a new project, click the 'New Project' button at the bottom left. Name your project. The toolbox automatically gives each project the prefix ‘SAP_’ (Sector Analysis Project). The project contains the folders ‘Original’, ‘Processed’ and ‘Staged’. The original, high resolution petal images should be saved into ‘Original’, and the resized images (resolution 2250x1500 pixels) saved into ‘Processed’. The SAT allows images to be resizes and processed under Image Processing, which searches for JPEG images in the Original folder and outputs to the Processed folder Within these folders, there can be another layer of folders, each containing all the images for one plant.
Once a project has been created, you can return to that project either by selecting that project in the ‘Current Directory’ line at the top of the Matlab window, or by opening the toolbox and using the ‘Browse’ button to select your project.
2 Segmenting The clones
Click the button ‘Segment Images’. Select the images you would like to segment. Choose the appropriate algorithm from the pop-up window – for the petals this should be AIH (AI Hanna’s algorithm – should be used generally) (AG is A-G Rolland-Lagan’s algorithm which was used in analysis of the dorsal lobe ref). For Arabidopsis GFP sector images use amelia_petal_sectors.m. A task bar indicates progress, and which image is being processed. When an image has been segmented, the image file in the ‘Staged’ folder is replaced by a folder with containing a matlab file called ‘edge_xy’ (the organ outline coordinates), a .jpg snapshot of the original image, a .tif black and white (binary) image with the suffix ‘_organ’ (corresponding to the petal/leaf outline), and a .tif binary image with the suffix ‘_sectors’ (corresponding to the sectors).