/** * MRI Leaf Infection Tools * * written 2012 by Volker Baecker (INSERM) at Montpellier RIO Imaging (www.mri.cnrs.fr) */ var helpURL = "http://dev.mri.cnrs.fr/wiki/imagej-macros/Leaf_Infection_Tools"; var greenChannel = "GFP"; var redChannel = "RFP"; var thresholdingMethod = "Huang"; var isCalculateCorrelation = true; var isCountAreas = true; var minSize = 10; macro "Unused Tool - C037" { } macro "MRI Leaf Infection Tools Help Action Tool - Cf00D18D19D28D29D38D73D74D83D84D9aD9bDaaDabCfffD00D01D0dD0eD0fD10D1eD1fD20D2eD2fD30D3eD3fD40D4fD50D5fD60D6fD70D80D90Da0Db0DbfDc0Dc1Dc2Dc3Dc4DceDcfDd0Dd1Dd2Dd3Dd4DddDdeDdfDe0De1De2De3De4DebDecDedDeeDefDf0Df1Df2Df3Df4Df5Df9DfaDfbDfcDfdDfeDffC0f0D02D03D06D07D08D09D0aD0cD11D12D13D14D1cD1dD21D22D23D24D25D2bD2cD2dD31D33D34D35D3bD3cD3dD41D44D45D46D4aD4bD4cD4eD51D52D53D56D57D59D5aD5bD5eD61D62D63D64D67D69D6aD6dD6eD71D72D75D79D7cD7dD7eD7fD81D82D85D86D8bD8cD8dD8fD91D93D94D95D96D97D99D9cD9fDa1Da6Da7Da9DaeDafDb1Db2Db3Db4Db7Db9DbaDbdDbeDc5Dc7Dc9DccDcdDd5DdaDdbDdcDe5De8De9DeaDf6Df8C888D04D05D0bD15D16D17D1aD1bD26D27D2aD32D36D37D39D3aD42D43D47D48D49D4dD54D55D58D5cD5dD65D66D68D6bD6cD76D77D78D7aD7bD87D88D89D8aD8eD92D98D9dD9eDa2Da3Da4Da5Da8DacDadDb5Db6Db8DbbDbcDc6Dc8DcaDcbDd6Dd7Dd8Dd9De6De7Df7"{ run('URL...', 'url='+helpURL); } macro "adjust display Action Tool - C037T4d14a" { run("Grays"); run("Enhance Contrast", "saturated=0.35"); } macro "measure Action Tool - C037T4d14m" { setBatchMode(true); title = getTitle(); inDir = getDirectory("image"); outDir = inDir + "/" + "control"; if (!File.exists(outDir)) File.makeDirectory(outDir); titleRed = replace(title, greenChannel, redChannel); run("Set Measurements...", "area perimeter display redirect=None decimal=3"); nr = roiManager("count"); correlation = newArray(nr / 2); numberOfAreasGreen = newArray(nr / 2); numberOfAreasRed = newArray(nr / 2); for (i=0; i