CellProfiler Pipeline: http://www.cellprofiler.org Version:1 SVNRevision:11710 LoadImages:[module_num:1|svn_version:\'11587\'|variable_revision_number:11|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?:None 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: Select subfolders to analyze: Image count:1 Text that these images have in common (case-sensitive):.tif 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 Load the input as images or objects?:Images Name this loaded image:original Name this loaded object:Nuclei Retain outlines of loaded objects?:No Name the outline image:LoadedImageOutlines Channel number:1 Rescale intensities?:Yes UnmixColors:[module_num:2|svn_version:\'10829\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D] Stain count:2 Color image:original Image name:Hematoxylin Stain:Hematoxylin Red absorbance:0.5 Green absorbance:0.5 Blue absorbance:0.5 Image name:Eosin Stain:Eosin Red absorbance:0.5 Green absorbance:0.5 Blue absorbance:0.5 Smooth:[module_num:3|svn_version:\'10465\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D] Select the input image:Hematoxylin Name the output image:blur1 Select smoothing method:Gaussian Filter Calculate artifact diameter automatically?:No Typical artifact diameter, in pixels:8 Edge intensity difference:0.1 RescaleIntensity:[module_num:4|svn_version:\'6746\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D] Select the input image:blur1 Name the output image:hematoxylin_rescaled Select rescaling method:Choose specific values to be reset to the full intensity range How do you want to calculate the minimum intensity?:Custom How do you want to calculate the maximum intensity?:Custom Enter the lower limit for the intensity range for the input image:0 Enter the upper limit for the intensity range for the input image:1 Enter the intensity range for the input image:0.34,0.48 Enter the desired intensity range for the final, rescaled image:0.000000,1.000000 Select method for rescaling pixels below the lower limit:Set to zero Enter custom value for pixels below lower limit:0 Select method for rescaling pixels above the upper limit:Set to one Enter custom value for pixels below upper limit:0 Select image to match in maximum intensity:None Enter the divisor:1 Select the measurement to use as a divisor:None Smooth:[module_num:5|svn_version:\'10465\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D] Select the input image:hematoxylin_rescaled Name the output image:blur2 Select smoothing method:Gaussian Filter Calculate artifact diameter automatically?:No Typical artifact diameter, in pixels:8 Edge intensity difference:0.2 IdentifyPrimaryObjects:[module_num:6|svn_version:\'10826\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D] Select the input image:blur2 Name the primary objects to be identified:Nuclei Typical diameter of objects, in pixel units (Min,Max):15,90 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:RobustBackground Adaptive Threshold correction factor:.8 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 SaveImages:[module_num:7|svn_version:\'10822\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D] Select the type of image to save:Objects Select the image to save:None Select the objects to save:Nuclei Select the module display window to save:None Select method for constructing file names:From image filename Select image name for file prefix:original Enter single file name:OrigBlue Do you want to add a suffix to the image file name?:No Text to append to the image name: Select file format to use:tif Output file location:Default Output Folder\x7CNone Image bit depth:8 Overwrite existing files without warning?:No Select how often to save:Every cycle Rescale the images? :No Save as grayscale or color image?:Color Select colormap:Spectral Store file and path information to the saved image?:No Create subfolders in the output folder?:No