CellProfiler Pipeline: http://www.cellprofiler.org Version:1 SVNRevision:11710 LoadImages:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D] File type to be loaded:tif,tiff,flex,zvi movies File selection method:Text-Regular expressions 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):\\d{6}_\\w+_\\d{2}_cell_\\w{2}_\\d{5}.tiff 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:Raw_Cells Name this loaded object:Nuclei Retain outlines of loaded objects?:No Name the outline image:LoadedImageOutlines Channel number:1 Rescale intensities?:No RescaleIntensity:[module_num:2|svn_version:\'6746\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D] Select the input image:Raw_Cells Name the output image:Scaled_Cells Select rescaling method:Stretch each image to use 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:0.000000,1.000000 Enter the desired intensity range for the final, rescaled image:0.000000,1.000000 Select method for rescaling pixels below the lower limit:Mask pixels Enter custom value for pixels below lower limit:0 Select method for rescaling pixels above the upper limit:Mask pixels 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 IdentifyPrimaryObjects:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D] Select the input image:Scaled_Cells Name the primary objects to be identified:ID_Cells Typical diameter of objects, in pixel units (Min,Max):30,80 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:0.9 Lower and upper bounds on threshold:0.17,1.0 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:Cell_Outlines 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 MeasureObjectSizeShape:[module_num:4|svn_version:\'1\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D] Select objects to measure:ID_Cells Calculate the Zernike features?:Yes MeasureObjectRadialDistribution:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D] Hidden:1 Hidden:1 Hidden:1 Select an image to measure:Raw_Cells Select objects to measure:ID_Cells Object to use as center?:These objects Select objects to use as centers:None Number of bins:8 MeasureTexture:[module_num:6|svn_version:\'1\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D] Hidden:1 Hidden:1 Hidden:3 Select an image to measure:Raw_Cells Select objects to measure:ID_Cells Texture scale to measure:3 Texture scale to measure:10 Texture scale to measure:20 Measure Gabor features?:Yes Number of angles to compute for Gabor:4 ConvertObjectsToImage:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D] Select the input objects:ID_Cells Name the output image:Cell_Image Select the color type:Binary (black & white) Select the colormap:Default SaveImages:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D] Select the type of image to save:Image Select the image to save:Cell_Image 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:Raw_Cells 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\x7C/Cells 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 ExportToDatabase:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:20|show_window:True|notes:\x5B\x5D] Database type:SQLite Database name:DefaultDB Add a prefix to table names?:No Table prefix:Expt_ SQL file prefix:SQL_ Output file location:Default Output Folder\x7CNone Create a CellProfiler Analyst properties file?:Yes Database host: Username: Password: Name the SQLite database file:DefaultDB.db Calculate the per-image mean values of object measurements?:Yes Calculate the per-image median values of object measurements?:No Calculate the per-image standard deviation values of object measurements?:No Calculate the per-well mean values of object measurements?:No Calculate the per-well median values of object measurements?:No Calculate the per-well standard deviation values of object measurements?:No Export measurements for all objects to the database?:All Select the objects: Maximum # of characters in a column name:64 Create one table per object or a single object table?:Single object table Enter an image url prepend if you plan to access your files via http: Write image thumbnails directly to the database?:Yes Select the images you want to save thumbnails of:Cell_Image Auto-scale thumbnail pixel intensities?:Yes Select the plate type:None Select the plate metadata:None Select the well metadata:None Include information for all images, using default values?:Yes Hidden:1 Hidden:1 Hidden:0 Select an image to include:None Use the image name for the display?:Yes Image name:Channel1 Channel color:red Do you want to add group fields?:No Enter the name of the group: Enter the per-image columns which define the group, separated by commas:ImageNumber, Image_Metadata_Plate, Image_Metadata_Well Do you want to add filter fields?:No Automatically create a filter for each plate?:No