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only_classification.cp
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CellProfiler Pipeline: http://www.cellprofiler.org
Version:1
SVNRevision:11710
LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D]
Input data file location:Elsewhere...\x7CC\x3A\\Users\\Sissela\\Documents\\MATLAB
Name of the file:Only_Classification_Slides.csv
Load images based on this data?:Yes
Base image location:Elsewhere...\x7CC\x3A\\Users\\Sissela\\Documents\\MATLAB\\08-tophats-registered\\slideA
Process just a range of rows?:No
Rows to process:1,100000
Group images by metadata?:No
Select metadata fields for grouping:position
Rescale intensities?:Yes
IdentifyPrimaryObjects:[module_num:2|svn_version:\'10826\'|variable_revision_number:8|show_window:False|notes:\x5B\x5D]
Select the input image:DO
Name the primary objects to be identified:blobs
Typical diameter of objects, in pixel units (Min,Max):2,10
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
Select the thresholding method:Manual
Threshold correction factor:1
Lower and upper bounds on threshold:0.000000,1.000000
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:1
Suppress local maxima that are closer than this minimum allowed distance:3
Speed up by using lower-resolution image to find local maxima?:No
Name the outline image:BlobOutlines
Fill holes in identified objects?:Yes
Automatically calculate size of smoothing filter?:No
Automatically calculate minimum allowed distance between local maxima?:No
Manual threshold:0.05
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:False|notes:\x5B\x5D]
Hidden:17
Select an image to measure:1_1
Select an image to measure:1_2
Select an image to measure:1_3
Select an image to measure:1_4
Select an image to measure:2_1
Select an image to measure:2_2
Select an image to measure:2_3
Select an image to measure:2_4
Select an image to measure:3_1
Select an image to measure:3_2
Select an image to measure:3_3
Select an image to measure:3_4
Select an image to measure:4_1
Select an image to measure:4_2
Select an image to measure:4_3
Select an image to measure:4_4
Select an image to measure:DO
Select objects to measure:blobs
ExportToSpreadsheet:[module_num:4|svn_version:\'10880\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D]
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?:No
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?:No
Calculate the per-image median values for object measurements?:No
Calculate the per-image standard deviation values for object measurements?:No
Output file location:Default Output Folder\x7CC\x3A\\\\Users\\\\User\\\\Documents\\\\MATLAB\\\\cells\\\\figs
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:blobs\x7CIntensity_MaxIntensity_DO,blobs\x7CIntensity_MaxIntensity_1_1,blobs\x7CIntensity_MaxIntensity_1_3,blobs\x7CIntensity_MaxIntensity_1_2,blobs\x7CIntensity_MaxIntensity_1_4,blobs\x7CIntensity_MaxIntensity_3_1,blobs\x7CIntensity_MaxIntensity_3_3,blobs\x7CIntensity_MaxIntensity_3_2,blobs\x7CIntensity_MaxIntensity_3_4,blobs\x7CIntensity_MaxIntensity_2_1,blobs\x7CIntensity_MaxIntensity_2_3,blobs\x7CIntensity_MaxIntensity_2_2,blobs\x7CIntensity_MaxIntensity_2_4,blobs\x7CIntensity_MaxIntensity_4_1,blobs\x7CIntensity_MaxIntensity_4_3,blobs\x7CIntensity_MaxIntensity_4_2,blobs\x7CIntensity_MaxIntensity_4_4,blobs\x7CLocation_Center_Y,blobs\x7CLocation_Center_X
Data to export:blobs
Combine these object measurements with those of the previous object?:No
File name:blobs.csv
Use the object name for the file name?:No