CellProfiler Pipeline: http://www.cellprofiler.org Version:1 SVNRevision:10847 LoadImages:[module_num:1|svn_version:\'10824\'|variable_revision_number:10|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?:Yes Input image file location:Default Input Folder\x7CNone Check image sets for missing or duplicate files?:Yes Group images by metadata?:Yes Exclude certain files?:No Specify metadata fields to group by:Timepoint Image count:1 Text that these images have in common (case-sensitive):_w1 Position of this image in each group:1 Extract metadata from where?:None Regular expression that finds metadata in the file name:_t(?P\x5B0-9\x5D+)_ Type the regular expression that finds metadata in the subfolder path:.\x5B\\\\/\x5Dsite(?P\x5B0-9\x5D+) Channel count:1 Group the movie frames?:Yes Grouping method:Separated Number of channels per group:2 Load the input as images or objects?:Images Name this loaded image:WL1_Nuclei Name this loaded object:Nuclei Retain outlines of loaded objects?":No Name the outline image:NucleiOutlines Channel number:1 Rescale intensities?:Yes IdentifyPrimaryObjects:[module_num:2|svn_version:\'10826\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D] Select the input image:WL1_Nuclei Name the primary objects to be identified:Nuclei Typical diameter of objects, in pixel units (Min,Max):7,55 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:1.2 Lower and upper bounds on threshold:0.000000,1.000000 Approximate fraction of image covered by objects?:0.01 Method to distinguish clumped objects:None 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:NucleiOutlines 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?:Yes 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 MeasureObjectIntensity:[module_num:3|svn_version:\'10816\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D] Hidden:1 Select an image to measure:WL1_Nuclei Select objects to measure:Nuclei MeasureObjectSizeShape:[module_num:4|svn_version:\'1\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D] Select objects to measure:Nuclei Calculate the Zernike features?:Yes TrackObjects:[module_num:5|svn_version:\'10629\'|variable_revision_number:4|show_window:True|notes:\x5B\x5D] Choose a tracking method:Overlap Select the objects to track:Nuclei Select object measurement to use for tracking:Number_Object_Number Maximum pixel distance to consider matches:15 Select display option:Color and Number Save color-coded image?:Yes Name the output image:TrackedCellsTIFF Select the motion model:Both Number of standard deviations for search radius:3 Search radius limit, in pixel units (Min,Max):2,10 Run the second phase of the LAP algorithm?:Yes Gap cost:100 Split alternative cost:40 Merge alternative cost:200 Maximum gap displacement:50 Maximum split score:50 Maximum merge score:50 Maximum gap:1 ExportToSpreadsheet:[module_num:6|svn_version:\'10787\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D] Select or enter the column delimiter:Tab Prepend the output file name to the data file names?:Yes Add image metadata columns to your object data file?:Yes Limit output to a size that is allowed in Excel?:No Select the columns of measurements to export?:No Calculate the per-image mean values for object measurements?:Yes Calculate the per-image median values for object measurements?:Yes Calculate the per-image standard deviation values for object measurements?:Yes Output file location:Default Output Folder\x7CNone Create a GenePattern GCT file?:No Select source of sample row name:Metadata Select the image to use as the identifier:None Select the metadata to use as the identifier:None Export all measurements, using default file names?:Yes Press button to select measurements to export: Data to export:Do not use Combine these object measurements with those of the previous object?:No File name:DATA.csv Use the object name for the file name?:Yes SaveImages:[module_num:7|svn_version:\'10822\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D] Select the type of image to save:Image Select the image to save:TrackedCellsTIFF Select the objects to save:None Select the module display window to save:None Select method for constructing file names:From image filename Select image name for file prefix:WL1_Nuclei 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:bmp Output file location:Default Output Folder\x7CNone Image bit depth:8 Overwrite existing files without warning?:Yes Select how often to save:Every cycle Rescale the images? :No Save as grayscale or color image?:Grayscale Select colormap:gray Store file and path information to the saved image?:Yes Create subfolders in the output folder?:No CreateBatchFiles:[module_num:8|svn_version:\'10375\'|variable_revision_number:4|show_window:True|notes:\x5B\x5D] Store batch files in default output folder?:Yes Output folder path:/cluster/home/biol/elahunt/OUT Are the cluster computers running Windows?:No Hidden\x3A in batch mode:No Hidden\x3A default input folder at time of save:/cluster/home/biol/elahunt/TIFF Hidden\x3A SVN revision number:0 Local root path:/cluster/home/biol/elahunt/TIFF Cluster root path:/cluster/home/biol/elahunt/TIFF