/** * Phase Contrast Cell Analysis Tool * Collaborators: * Damien Planchon * * Segment and measure cells in phase contrast images * * (c) 2014 INSERM * written by Volker Baecker at Montpellier RIO Imaging (www.mri.cnrs.fr) * */ var _CROP_RECT_X = 0; var _CROP_RECT_Y = 34; var _CROP_RECT_WIDTH = 757; var _CROP_RECT_HEIGHT = 469; var _CONVERT_TO_8BIT = true; var _BATCH_MODE = false; var _CLASSIFIERS_DIR = getDirectory("imagej") + "models"; var _CLASSIFIERS = getFileList(_CLASSIFIERS_DIR); var _CLASSIFIER = _CLASSIFIERS[0]; var _EXCLUDE_SMALL_OBJECTS = true; var _MIN_SIZE = 10; var _FILL_HOLES = false; var _SELECTION_WIDTH = 1; var _FILE_EXT = ".tif"; var _DIR = ""; var _URL = "http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Phase_Contrast_Cell_Analysis_Tool_%28Trainable_WEKA_Segmentation%29"; macro "HELP for the MRI Phase Contrast Cell Analysis Action Tool - Cf00D00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D11D12D13D14D15D16D17D18D19D1aD1bD1cD1eD1fD20D21D22D23D24D26D27D28D29DaD2bD2cD2eD2fD30D31D34D36D37D38D39D3aD3bD3cD3eD3fD40D41D42D43D44D45D46D47D49D4aD4bD4cD4dD4eD4fD50D51D52D53D54D55D56D57D5aD5bD5cD5dD5eD5fD60D61D62D63D64D6aD6bD6cD6dD6eD6fD70D71D72D73D74D75D76D7aD7bD7cD7dD7eD7fD80D81D82D83D84D85D8bD8cD8dD8eD8fD90D91D92D93D94D9bD9dD9eD9fDa0Da1Da2Da4Da5Da6Da7Da9DaaDabDacDadDaeDafDb0Db3Db4Db5Db6Db7Db8Db9DbaDbbDbcDbdDbeDbfDc0Dc1Dc2Dc3Dc4Dc8Dc9DcaDcbDccDcdDceDcfDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd8Dd9DddDdeDdfDe0De1De2De3De4De5De6De7De8De9DeaDebDecDedDeeDefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC4f8D1dD25D2dD32D33D35D3dD48D58D59D65D66D67D68D69D77D78D79D86D87D88D89D8aD95D96D97D98D99D9aD9cDa3Da8Db1Db2Dc5Dc6Dc7Dd7DdaDdbDdc" { run('URL...', 'url='+_URL); } macro "Preprocessing Action Tool - C037T4d14p" { dir = getDirectory(""); files = getFileList(dir); out = "cropped"; File.mkdir(dir + out); print("\\Clear"); if (_BATCH_MODE) setBatchMode(true); count = countImages(files); print("preprocessing started on folder: " + dir); counter = 1; for(i=0; i