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cytoplasmic_intensity.cppipe
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cytoplasmic_intensity.cppipe
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CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:20150910190903
GitHash:207f5bf
ModuleCount:7
HasImagePlaneDetails:False
LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Loads data from URL; intended for use with image lists generated by Jenkins.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Input data file location:URL\x7C
URL of the file:http\x3A//localhost\x3A8080/userContent/cp_imageLists/cytoplasmic_intensity_imageList.csv
Load images based on this data?:Yes
Base image location:Default Input Folder\x7CNone
Process just a range of rows?:No
Rows to process:1,100000
Group images by metadata?:No
Select metadata tags for grouping:Barcode,RowNumber,Column
Rescale intensities?:Yes
IdentifyPrimaryObjects:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:10|show_window:False|notes:\x5B\'Nuclear segmentation. Adjust "threshold correction factor" as needed (0-1 more lenient, greater than 1 more stringent).\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Nuclei
Name the primary objects to be identified:Nuclei
Typical diameter of objects, in pixel units (Min,Max):20,90
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?:Yes
Method to distinguish clumped objects:Shape
Method to draw dividing lines between clumped objects:Shape
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?: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
Handling of objects if excessive number of objects identified:Continue
Maximum number of objects:500
Threshold setting version:1
Threshold strategy:Global
Thresholding method:Otsu
Select the smoothing method for thresholding:Automatic
Threshold smoothing scale:1
Threshold correction factor:1
Lower and upper bounds on threshold:0.000000,1.000000
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:From image
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
Use default parameters?:Default
Lower outlier fraction:0.05
Upper outlier fraction:0.05
Averaging method:Mean
Variance method:Standard deviation
# of deviations:2.0
RescaleIntensity:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'DEFINE CELL BOUNDARY BY BACKGROUND FLUORESCENCE IN NUCLEAR STAIN CHANNEL\x3A Rescales DNA image to exaggerate background staining of cytoplasm. Check intensity of test images (cytoplasm vs background) and adjust "intensity range for the input image" accordingly. Output should enhance the contrast between cytoplasm and background.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Nuclei
Name the output image:Rescaled_DNA
Rescaling method:Choose specific values to be reset to the full intensity range
Method to calculate the minimum intensity:Custom
Method to calculate the maximum intensity:Custom
Lower intensity limit for the input image:0
Upper intensity limit for the input image:0.07
Intensity range for the input image:0.0,0.1
Intensity range for the output image:0.000000,1.000000
Method to rescale pixels below the lower limit:Set to zero
Custom value for pixels below lower limit:0
Method to rescale pixels above the upper limit:Set to one
Custom value for pixels above upper limit:0
Select image to match in maximum intensity:None
Divisor value:1
Divisor measurement:None
IdentifyPrimaryObjects:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:10|show_window:False|notes:\x5B\'DEFINE CELL BOUNDARY BY BACKGROUND FLUORESCENCE IN NUCLEAR STAIN CHANNEL\x3A Segments cytoplasm. Adjust "threshold correction factor" as needed (0-1 more lenient, greater than 1 more stringent).\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Rescaled_DNA
Name the primary objects to be identified:Cytoplasm_plus_Nuclei
Typical diameter of objects, in pixel units (Min,Max):40,400
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
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: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
Handling of objects if excessive number of objects identified:Continue
Maximum number of objects:500
Threshold setting version:1
Threshold strategy:Global
Thresholding method:Otsu
Select the smoothing method for thresholding:Automatic
Threshold smoothing scale:1
Threshold correction factor:0.6
Lower and upper bounds on threshold:0.000000,1.000000
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:From image
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
Use default parameters?:Default
Lower outlier fraction:0.05
Upper outlier fraction:0.05
Averaging method:Mean
Variance method:Standard deviation
# of deviations:2.0
IdentifyTertiaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'Subtracts nuclei from cell boundary to leave cytoplasm.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the larger identified objects:Cytoplasm_plus_Nuclei
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?:No
Shrink smaller object prior to subtraction?:Yes
MeasureObjectIntensity:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Adds intensity measures for cytoplasm+nuclei, cytoplasm only, and nuclei only.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Hidden:1
Select an image to measure:pAKT
Select objects to measure:Cytoplasm_plus_Nuclei
Select objects to measure:Cytoplasm
Select objects to measure:Nuclei
ExportToSpreadsheet:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\'Export module required for Jenkins.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the column delimiter:Comma (",")
Add image metadata columns to your object data file?:Yes
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?: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 measurement types?:No
:
Representation of Nan/Inf:NaN
Add a prefix to file names?:No
Filename prefix\x3A:MyExpt_
Overwrite existing files without warning?:Yes
Data to export:Image
Combine these object measurements with those of the previous object?:No
File name:\\\\g<Barcode>_\\\\g<RowNumber>_\\\\g<Column>.csv
Use the object name for the file name?:No