CellProfiler Pipeline: http://www.cellprofiler.org Version:3 DateRevision:20151022101140 GitHash:Unknown rev. ModuleCount:22 HasImagePlaneDetails:False LoadImages:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] File type to be loaded:individual images 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\x7C Check image sets for unmatched 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:2 Text that these images have in common (case-sensitive):DAPI 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:DNA Name this loaded object:Nuclei Retain outlines of loaded objects?:No Name the outline image:LoadedImageOutlines Channel number:1 Rescale intensities?:Yes Text that these images have in common (case-sensitive):GFP Position of this image in each group:2 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:IntPathogen Name this loaded object:Nuclei Retain outlines of loaded objects?:No Name the outline image:LoadedImageOutlines Channel number:1 Rescale intensities?:Yes LoadSingleImage:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Input image file location:Default Output Folder\x7C/home/emmenlau/TargetInfectX/Projects/Brucella/JOVEPublication/Results/0BCDAC-T107-Full-SCpart1 Filename of the image to load (Include the extension, e.g., .tif):IllumDNA_0bCDac-T103.mat Load as images or objects?:Images Name the image that will be loaded:IllumDNA Name this loaded object:Nuclei Retain outlines of loaded objects?:No Name the outlines:NucleiOutlines Rescale intensities?:No Filename of the image to load (Include the extension, e.g., .tif):IllumPathogen_0bCDac-T103.mat Load as images or objects?:Images Name the image that will be loaded:IllumPathogen Name this loaded object:Nuclei Retain outlines of loaded objects?:No Name the outlines:NucleiOutlines Rescale intensities?:No CorrectIlluminationApply:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the input image:DNA Name the output image:Corr0DNA Select the illumination function:IllumDNA Select how the illumination function is applied:Divide Select the input image:IntPathogen Name the output image:Corr0IntPathogen Select the illumination function:IllumPathogen Select how the illumination function is applied:Divide ImageMath:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Operation:None Raise the power of the result by:1.0 Multiply the result by:1.0 Add to result:0.0 Set values less than 0 equal to 0?:Yes Set values greater than 1 equal to 1?:Yes Ignore the image masks?:Yes Name the output image:Corr1DNA Image or measurement?:Image Select the first image:Corr0DNA Multiply the first image by:16.0 Measurement: Image or measurement?:Image Select the second image:DNA Multiply the second image by:0.0 Measurement: ImageMath:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Operation:None Raise the power of the result by:1.0 Multiply the result by:1.0 Add to result:0.0 Set values less than 0 equal to 0?:Yes Set values greater than 1 equal to 1?:Yes Ignore the image masks?:Yes Name the output image:Corr1IntPathogen Image or measurement?:Image Select the first image:Corr0IntPathogen Multiply the first image by:16.0 Measurement: Image or measurement?:Image Select the second image: Multiply the second image by:1.0 Measurement: IdentifyPrimaryObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:10|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:True] Select the input image:Corr1DNA Name the primary objects to be identified:Nuclei Typical diameter of objects, in pixel units (Min,Max):16,64 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?:No 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:7.0 Speed up by using lower-resolution image to find local maxima?:Yes Name the outline image:PrimaryOutlines Fill holes in identified objects?:After both thresholding and declumping Automatically calculate size of smoothing filter for declumping?:Yes Automatically calculate minimum allowed distance between local maxima?:Yes Retain outlines of the identified objects?:No Automatically calculate the threshold using the Otsu method?:Yes Enter Laplacian of Gaussian threshold:0.5 Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes Enter LoG filter diameter:5.0 Handling of objects if excessive number of objects identified:Continue Maximum number of objects:1000 Threshold setting version:1 Threshold strategy:Global Thresholding method:Otsu Select the smoothing method for thresholding:Automatic Threshold smoothing scale:1.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.1,1.0 Approximate fraction of image covered by objects?:0.01 Manual threshold:0.0 Select the measurement to threshold with:None Select binary image:None Masking objects:None 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 Method to calculate adaptive window size:Image size Size of adaptive window:10 ExpandOrShrinkObjects:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the input objects:Nuclei Name the output objects:VoronoiCells Select the operation:Expand objects by a specified number of pixels Number of pixels by which to expand or shrink:25 Fill holes in objects so that all objects shrink to a single point?:No Retain the outlines of the identified objects?:No Name the outline image:ShrunkenNucleiOutlines IdentifyPrimaryObjects:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:10|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:True] Select the input image:Corr1IntPathogen Name the primary objects to be identified:IntPathogen Typical diameter of objects, in pixel units (Min,Max):1,16 Discard objects outside the diameter range?:No Try to merge too small objects with nearby larger objects?:No Discard objects touching the border of the image?:No 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:7.0 Speed up by using lower-resolution image to find local maxima?:Yes Name the outline image:PrimaryOutlines Fill holes in identified objects?:Never Automatically calculate size of smoothing filter for declumping?:Yes Automatically calculate minimum allowed distance between local maxima?:Yes Retain outlines of the identified objects?:No Automatically calculate the threshold using the Otsu method?:Yes Enter Laplacian of Gaussian threshold:0.5 Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes Enter LoG filter diameter:5.0 Handling of objects if excessive number of objects identified:Continue Maximum number of objects:10000 Threshold setting version:1 Threshold strategy:Global Thresholding method:MoG Select the smoothing method for thresholding:Automatic Threshold smoothing scale:1.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.1,1.0 Approximate fraction of image covered by objects?:0.001 Manual threshold:0.0 Select the measurement to threshold with:None Select binary image:None Masking objects:None 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 Method to calculate adaptive window size:Image size Size of adaptive window:10 MeasureObjectIntensity:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Hidden:1 Select an image to measure:Corr1IntPathogen Select objects to measure:IntPathogen MeasureObjectSizeShape:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select objects to measure:IntPathogen Calculate the Zernike features?:No FilterObjects:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:True] Name the output objects:TrueIntPathogen Select the object to filter:IntPathogen Select the filtering mode:Measurements Select the filtering method:Limits Select the objects that contain the filtered objects:None Retain outlines of the identified objects?:No Name the outline image:FilteredObjects Rules file location:Elsewhere...\x7C Rules file name:rules.txt Class number:1 Measurement count:2 Additional object count:0 Assign overlapping child to:Both parents Select the measurement to filter by:AreaShape_Area Filter using a minimum measurement value?:Yes Minimum value:2.0 Filter using a maximum measurement value?:No Maximum value:64 Select the measurement to filter by:Intensity_UpperQuartileIntensity_Corr1IntPathogen Filter using a minimum measurement value?:Yes Minimum value:0.15 Filter using a maximum measurement value?:No Maximum value:1.0 MeasureObjectIntensity:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Hidden:1 Select an image to measure:Corr1IntPathogen Select objects to measure:TrueIntPathogen RelateObjects:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the input child objects:TrueIntPathogen Select the input parent objects:VoronoiCells Calculate child-parent distances?:None Calculate per-parent means for all child measurements?:Yes Calculate distances to other parents?:No Parent name:None FilterObjects:[module_num:14|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\'\\t\\t\\t\\t\\t\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Name the output objects:InfectedCells Select the object to filter:VoronoiCells Select the filtering mode:Measurements Select the filtering method:Limits Select the objects that contain the filtered objects:None Retain outlines of the identified objects?:No Name the outline image:FilteredObjects Rules file location:Elsewhere...\x7C Rules file name:rules.txt Class number:1 Measurement count:1 Additional object count:0 Assign overlapping child to:Both parents Select the measurement to filter by:Children_TrueIntPathogen_Count Filter using a minimum measurement value?:Yes Minimum value:1.0 Filter using a maximum measurement value?:No Maximum value:1.0 FilterObjects:[module_num:15|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Name the output objects:TrueIntPathogenInCells Select the object to filter:TrueIntPathogen Select the filtering mode:Measurements Select the filtering method:Limits Select the objects that contain the filtered objects:None Retain outlines of the identified objects?:No Name the outline image:FilteredObjects Rules file location:Elsewhere...\x7C Rules file name:rules.txt Class number:1 Measurement count:1 Additional object count:0 Assign overlapping child to:Both parents Select the measurement to filter by:Parent_VoronoiCells Filter using a minimum measurement value?:Yes Minimum value:1.0 Filter using a maximum measurement value?:No Maximum value:1.0 MeasureImageAreaOccupied:[module_num:16|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Hidden:1 Measure the area occupied in a binary image, or in objects?:Objects Select objects to measure:TrueIntPathogenInCells Retain a binary image of the object regions?:No Name the output binary image:Stain Select a binary image to measure:None ExportToSpreadsheet:[module_num:17|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:True] Select the column delimiter:Tab Add image metadata columns to your object data file?:No Limit output to a size that is allowed in Excel?:No Select the 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?:No Output file location:Default Output Folder\x7C 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 measurement types?:No Press button to select measurements to export: Representation of Nan/Inf:NaN Add a prefix to file names?:Yes Filename prefix\x3A: Overwrite without warning?:Yes Data to export:Image Combine these object measurements with those of the previous object?:No File name:BrucellaEntry.csv Use the object name for the file name?:No ImageMath:[module_num:18|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Operation:None Raise the power of the result by:0.7 Multiply the result by:1.0 Add to result:0.0 Set values less than 0 equal to 0?:Yes Set values greater than 1 equal to 1?:Yes Ignore the image masks?:Yes Name the output image:LogscaledDNA Image or measurement?:Image Select the first image:Corr1DNA Multiply the first image by:1.0 Measurement: Image or measurement?:Image Select the second image:CorrDNA Multiply the second image by:1.0 Measurement: ImageMath:[module_num:19|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Operation:None Raise the power of the result by:0.7 Multiply the result by:1.0 Add to result:0.0 Set values less than 0 equal to 0?:Yes Set values greater than 1 equal to 1?:Yes Ignore the image masks?:Yes Name the output image:LogscaledIntPathogen Image or measurement?:Image Select the first image:Corr1IntPathogen Multiply the first image by:1.0 Measurement: Image or measurement?:Image Select the second image: Multiply the second image by:1.0 Measurement: GrayToColor:[module_num:20|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select a color scheme:RGB Select the image to be colored red:Leave this black Select the image to be colored green:LogscaledIntPathogen Select the image to be colored blue:LogscaledDNA Name the output image:LogscaledDNAIntPathogen Relative weight for the red image:1.0 Relative weight for the green image:1.0 Relative weight for the blue image:1.0 Select the image to be colored cyan:Leave this black Select the image to be colored magenta:Leave this black Select the image to be colored yellow:Leave this black Select the image that determines brightness:Leave this black Relative weight for the cyan image:1.0 Relative weight for the magenta image:1.0 Relative weight for the yellow image:1.0 Relative weight for the brightness image:1.0 Select the input image to add to the stacked image:None OverlayOutlines:[module_num:21|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Display outlines on a blank image?:No Select image on which to display outlines:LogscaledDNAIntPathogen Name the output image:InfectedCellsOverlay Outline display mode:Color Select method to determine brightness of outlines:Max of image Width of outlines:1 Select outlines to display:None Select outline color:Red Load outlines from an image or objects?:Objects Select objects to display:VoronoiCells Select outlines to display:None Select outline color:green Load outlines from an image or objects?:Objects Select objects to display:InfectedCells SaveImages:[module_num:22|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:InfectedCellsOverlay 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:DNA Enter single file name:OrigBlue Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:Infected Saved file format:png Output file location:Default Output Folder\x7C Image bit depth:8 Overwrite existing files without warning?:Yes When to save:Every cycle Rescale the images? :Yes Save as grayscale or color image?:Grayscale Select colormap:gray Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...\x7C Saved movie format:avi