CellProfiler Pipeline: http://www.cellprofiler.org Version:2 DateRevision:20130610174950 LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Input data file location:Elsewhere...\x7CC\x3A\\\\CWorkspace\\\\CellProfiler\\\\ImageLists Name of the file:TEST01 _2013-10-08_20-05-14.csv Load images based on this data?:Yes Base image location:None\x7CNone Process just a range of rows?:No Rows to process:1,100000 Group images by metadata?:No Select metadata fields for grouping: Rescale intensities?:Yes IdentifyPrimaryObjects:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:9|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Select the input image:DAPI Name the primary objects to be identified:Nuclei Typical diameter of objects, in pixel units (Min,Max):14,55 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 Adaptive Threshold correction factor:0.9 Lower and upper bounds on threshold:0.000000,1.000000 Approximate fraction of image covered by objects?:0.01 Method to distinguish clumped objects:Shape Method to draw dividing lines between clumped objects:Propagate 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 Method to calculate adaptive window size:Image size Size of adaptive window:10 IdentifySecondaryObjects:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Select the input objects:Nuclei Name the objects to be identified:Cells Select the method to identify the secondary objects:Distance - B Select the input image:FITC Select the thresholding method:Otsu Global Threshold correction factor:0.6 Lower and upper bounds on threshold:0.000000,1.000000 Approximate fraction of image covered by objects?:0.01 Number of pixels by which to expand the primary objects:20 Regularization factor:0.05 Name the outline image:SecondaryOutlines Manual threshold:0.0 Select binary image:None Retain outlines of the identified secondary objects?:No 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 Discard secondary objects touching the border of the image?:No Discard the associated primary objects?:No Name the new primary objects:FilteredNuclei Retain outlines of the new primary objects?:No Name the new primary object outlines:FilteredNucleiOutlines Select the measurement to threshold with:None Fill holes in identified objects?:Yes Method to calculate adaptive window size:Image size Size of adaptive window:10 IdentifyTertiaryObjects:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Select the larger identified objects:Cells Select the smaller identified objects:Nuclei Name the tertiary objects to be identified:Cytoplasm Name the outline image:CytoplasmOutlines Retain outlines of the tertiary objects?:Yes Shrink primary object?:Yes MeasureObjectNeighbors:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Select objects to measure:Cells Select neighboring objects to measure:Cells Method to determine neighbors:Adjacent Neighbor distance:5 Retain the image of objects colored by numbers of neighbors for use later in the pipeline (for example, in SaveImages)?:No Name the output image:ObjectNeighborCount Select colormap:Default Retain the image of objects colored by percent of touching pixels for use later in the pipeline (for example, in SaveImages)?:No Name the output image:PercentTouching Select a colormap:Default MeasureImageIntensity:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Select the image to measure:FITC Measure the intensity only from areas enclosed by objects?:Yes Select the input objects:Nuclei MeasureObjectIntensity:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Hidden:1 Select an image to measure:FITC Select objects to measure:Cytoplasm Select objects to measure:Nuclei Select objects to measure:Cells MeasureObjectIntensity:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Hidden:1 Select an image to measure:DAPI Select objects to measure:Cytoplasm Select objects to measure:Nuclei MeasureImageIntensity:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Select the image to measure:FITC Measure the intensity only from areas enclosed by objects?:Yes Select the input objects:Cytoplasm CalculateMath:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Name the output measurement:TEST01 Ratio Operation:Divide Select the numerator measurement type:Image Select the numerator objects:None Select the numerator measurement:Intensity_MedianIntensity_FITC_Nuclei Multiply the above operand by:1 Raise the power of above operand by:1 Select the denominator measurement type:Image Select the denominator objects:None Select the denominator measurement:Intensity_MedianIntensity_FITC_Cytoplasm Multiply the above operand by:1 Raise the power of above operand by:1 Take log10 of result?:No Multiply the result by:1 Raise the power of result by:1 Add to the result:0 Constrain the result to a lower bound?:No Set values less than this to this value?:0 Constrain the result to an upper bound?:No Set values greater than this to this value?:1 CalculateMath:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Name the output measurement:TEST01 Levels Operation:Add Select the first operand measurement type:Image Select the first operand objects:None Select the first operand measurement:Intensity_MedianIntensity_FITC_Nuclei Multiply the above operand by:1 Raise the power of above operand by:1 Select the second operand measurement type:Image Select the second operand objects:None Select the second operand measurement:Intensity_MedianIntensity_FITC_Nuclei Multiply the above operand by:1 Raise the power of above operand by:1 Take log10 of result?:No Multiply the result by:1 Raise the power of result by:1 Add to the result:0 Constrain the result to a lower bound?:No Set values less than this to this value?:0 Constrain the result to an upper bound?:No Set values greater than this to this value?:1 CalculateMath:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Name the output measurement:TEST01 RatioNC Operation:Divide Select the numerator measurement type:Object Select the numerator objects:Nuclei Select the numerator measurement:Intensity_MedianIntensity_FITC Multiply the above operand by:1 Raise the power of above operand by:1 Select the denominator measurement type:Object Select the denominator objects:Cytoplasm Select the denominator measurement:Intensity_MedianIntensity_FITC Multiply the above operand by:1 Raise the power of above operand by:1 Take log10 of result?:No Multiply the result by:1 Raise the power of result by:1 Add to the result:0 Constrain the result to a lower bound?:No Set values less than this to this value?:0 Constrain the result to an upper bound?:No Set values greater than this to this value?:1 ExportToSpreadsheet:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)] Select or enter the column delimiter:Comma (",") Prepend the output file name to the data file names?:No 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?:Yes 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?:No Press button to select measurements to export:Image\x7CCount_Nuclei,Image\x7CFileName_DAPI,Image\x7CIntensity_MedianIntensity_FITC_Cytoplasm,Image\x7CIntensity_MedianIntensity_FITC_Nuclei,Image\x7CMath_TEST01 Levels,Image\x7CMath_TEST01 Ratio,Image\x7CMetadata_Column,Image\x7CMetadata_Barcode,Image\x7CMetadata_RowNumber,Nuclei\x7CIntensity_MeanIntensity_FITC,Nuclei\x7CIntensity_MeanIntensity_DAPI,Nuclei\x7CIntensity_MedianIntensity_FITC,Nuclei\x7CIntensity_MedianIntensity_DAPI,Nuclei\x7CIntensity_IntegratedIntensity_FITC,Nuclei\x7CIntensity_IntegratedIntensity_DAPI,Nuclei\x7CMath_TEST01 RatioNC,Cells\x7CNeighbors_PercentTouching_Adjacent,Cells\x7CNeighbors_NumberOfNeighbors_Adjacent,Cells\x7CIntensity_MedianIntensity_FITC,Cells\x7CIntensity_IntegratedIntensity_FITC Data to export:Image Combine these object measurements with those of the previous object?:No File name:Image_\\\\g_\\\\g_\\\\g_\\\\g.csv Use the object name for the file name?:No Data to export:Nuclei Combine these object measurements with those of the previous object?:No File name:Object_\\\\g_\\\\g_\\\\g_\\\\g.csv Use the object name for the file name?:No Data to export:Cells Combine these object measurements with those of the previous object?:Yes File name:DATA.csv Use the object name for the file name?:Yes