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\x7C. Check image sets for missing or duplicate files?: 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):16604_16602TA_KO10x01 Position of this image in each group:16604_16602TA_KO10x01 Extract metadata from where?:None Regular expression that finds metadata in the file name:None Type the regular expression that finds metadata in the subfolder path:None Channel count:1 Group the movie frames?:No Grouping method:Interleaved Number of channels per group:2 Load the input as images or objects?:Images Name this loaded image:Original_Image Name this loaded object:Nuclei Retain outlines of loaded objects?:No Name the outline image:NucleiOutlines Channel number:1 Rescale intensities?:Yes ImageMath:[module_num:2|svn_version:\'10718\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D] Operation:Invert Raise the power of the result by:1.0 Multiply the result by:1.0 Add to result:0 Set values less than 0 equal to 0?:No Set values greater than 1 equal to 1?:No Ignore the image masks?:No Name the output image:Inverted4Area Image or measurement?:Image Select the first image:Original_Image Multiply the first image by:1.0 Measurement: Image or measurement?:Image Select the second image: Multiply the second image by:1 Measurement: CorrectIlluminationCalculate:[module_num:3|svn_version:\'10458\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D] Select the input image:Original_Image Name the output image:IllumFunc Select how the illumination function is calculated:Regular Dilate objects in the final averaged image?:No Dilation radius:0 Block size:60 Rescale the illumination function?:Yes Calculate function for each image individually, or based on all images?:Each Smoothing method:Median Filter Method to calculate smoothing filter size:Object size Approximate object size:10 Smoothing filter size:10 Retain the averaged image for use later in the pipeline (for example, in SaveImages)?:Yes Name the averaged image:Do not save Retain the dilated image for use later in the pipeline (for example, in SaveImages)?:Yes Name the dilated image:Do not save Automatically calculate spline parameters?:Yes Background mode:auto Number of spline points:5 Background threshold:2 Image resampling factor:2 Maximum number of iterations:40 Residual value for convergence:0.001 CorrectIlluminationApply:[module_num:4|svn_version:\'10300\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D] Select the input image:Original_Image Name the output image:Corrected_Original Select the illumination function:IllumFunc Select how the illumination function is applied:Divide ImageMath:[module_num:5|svn_version:\'10718\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D] Operation:Invert Raise the power of the result by:1.0 Multiply the result by:1.0 Add to result:0 Set values less than 0 equal to 0?:No Set values greater than 1 equal to 1?:No Ignore the image masks?:No Name the output image:InvertedGray Image or measurement?:Image Select the first image:Corrected_Original Multiply the first image by:1.0 Measurement: Image or measurement?:Image Select the second image: Multiply the second image by:1 Measurement: MeasureImageAreaOccupied:[module_num:6|svn_version:\'10563\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D] Hidden:1 Measure the area occupied in a binary image, or in objects?:Binary Image Select objects to measure:None Retain a binary image of the object regions?:No Name the output binary image:Stain Select a binary image to measure:None IdentifyPrimaryObjects:[module_num:7|svn_version:\'10826\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D] Select the input image:InvertedGray Name the primary objects to be identified:Nuclei Typical diameter of objects, in pixel units (Min,Max):4,35 Discard objects outside the diameter range?:Yes Try to merge too small objects with nearby larger objects?:Yes Discard objects touching the border of the image?:No Select the thresholding method:Otsu Global Threshold correction factor:1 Lower and upper bounds on threshold:0,1 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:5 Speed up by using lower-resolution image to find local maxima?:Yes Name the outline image:NucOutlines 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:Otsu Global Retain outlines of the identified objects?:Yes Automatically calculate the threshold using the Otsu method?:Yes Enter Laplacian of Gaussian threshold:.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 GrayToColor:[module_num:8|svn_version:\'10341\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D] Select a color scheme:CMYK Select the input image to be colored red:Original_Image Select the input image to be colored green:Original_Image Select the input image to be colored blue:Original_Image Name the output image:ColorImage Relative weight for the red image:1 Relative weight for the green image:1 Relative weight for the blue image:1 Select the input image to be colored cyan:None Select the input image to be colored magenta:None Select the input image to be colored yellow:None Select the input image that determines brightness:None Relative weight for the cyan image:1 Relative weight for the magenta image:1 Relative weight for the yellow image:1 Relative weight for the brightness image:1 Select the input image to add to the stacked image:None OverlayOutlines:[module_num:9|svn_version:\'10672\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D] Display outlines on a blank image?:No Select image on which to display outlines:ColorImage Name the output image:OverlaidOriginal Select outline display mode:Color Select method to determine brightness of outlines:Max possible Width of outlines:1 Select outlines to display:NucOutlines Select outline color:Green DisplayDataOnImage:[module_num:10|svn_version:\'10412\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D] Display object or image measurements?:Object Select the input objects:None Measurement to display:None Select the image on which to display the measurements:None Text color:red Name the output image that has the measurements displayed:DisplayImage Font size (points):10 Number of decimals:2 Image elements to save:Image DisplayDataOnImage:[module_num:11|svn_version:\'10412\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D] Display object or image measurements?:Object Select the input objects:None Measurement to display:None Select the image on which to display the measurements:None Text color:red Name the output image that has the measurements displayed:DisplayImage Font size (points):10 Number of decimals:2 Image elements to save:Image