CellProfiler Pipeline: http://www.cellprofiler.org Version:1 SVNRevision:10415 LoadImages:[module_num:1|svn_version:\'10372\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D] File type to be loaded:individual images File selection method:Text-Exact match Number of images in each group?:3 Type the text that the excluded images have in common:Do not use Analyze all subfolders within the selected folder?:No Input image file location:Default Input Folder\x7CNone Check image sets for missing or duplicate files?:Yes Group images by metadata?:No Exclude certain files?:No Specify metadata fields to group by: Image count:1 Text that these images have in common (case-sensitive):.jpg Position of this image in each group:1 Extract metadata from where?:None Regular expression that finds metadata in the file name:^(?P.*)_(?P\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P\x5B0-9\x5D) Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\/\x5D(?P.*)\x5B\\\\/\x5D(?P.*)$ Channel count:1 Group the movie frames?:No Grouping method:Interleaved Number of channels per group:3 Name this loaded image:DNA Channel number:1 IdentifyPrimaryObjects:[module_num:2|svn_version:\'10372\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D] Select the input image:DNA Name the primary objects to be identified:Nuclei Typical diameter of objects, in pixel units (Min,Max):10,40 Discard objects outside the diameter range?:Yes Try to merge too small objects with nearby larger objects?:No Discard objects touching the border of the image?:Yes Select the thresholding method:Otsu Global Threshold correction factor:1 Lower and upper bounds on threshold:0.000000,1.000000 Approximate fraction of image covered by objects?:0.01 Method to distinguish clumped objects:Intensity Method to draw dividing lines between clumped objects:Intensity Size of smoothing filter:10 Suppress local maxima that are closer than this minimum allowed distance:7 Speed up by using lower-resolution image to find local maxima?:Yes Name the outline image:PrimaryOutlines Fill holes in identified objects?:Yes Automatically calculate size of smoothing filter?:Yes Automatically calculate minimum allowed distance between local maxima?:Yes Manual threshold:0.0 Select binary image:None Retain outlines of the identified objects?:No Automatically calculate the threshold using the Otsu method?:Yes Enter Laplacian of Gaussian threshold:0.5 Two-class or three-class thresholding?:Two classes Minimize the weighted variance or the entropy?:Weighted variance Assign pixels in the middle intensity class to the foreground or the background?:Foreground Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes Enter LoG filter diameter:5 Handling of objects if excessive number of objects identified:Continue Maximum number of objects:500 Select the measurement to threshold with:None