qc_without_batchfile.cppipe

CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:20160418141927
GitHash:9969f42
ModuleCount:5
HasImagePlaneDetails:False

LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Input data file location:Default Input Folder\x7C
    Name of the file:
    Load images based on this data?:Yes
    Base image location:Default Input Folder\x7C
    Process just a range of rows?:No
    Rows to process:1,100000
    Group images by metadata?:Yes
    Select metadata tags for grouping:Plate,Well,Site
    Rescale intensities?:Yes

MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Calculate metrics for which images?:All loaded images
    Image count:1
    Scale count:4
    Threshold count:1
    Select the images to measure:
    Include the image rescaling value?:Yes
    Calculate blur metrics?:Yes
    Spatial scale for blur measurements:5
    Spatial scale for blur measurements:10
    Spatial scale for blur measurements:20
    Spatial scale for blur measurements:50
    Calculate saturation metrics?:Yes
    Calculate intensity metrics?:Yes
    Calculate thresholds?:No
    Use all thresholding methods?:Yes
    Select a thresholding method:Otsu
    Typical fraction of the image covered by objects:0.1
    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

MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Calculate metrics for which images?:Select...
    Image count:2
    Scale count:1
    Threshold count:1
    Scale count:1
    Threshold count:1
    Select the images to measure:OrigDNA
    Include the image rescaling value?:No
    Calculate blur metrics?:No
    Spatial scale for blur measurements:20
    Calculate saturation metrics?:No
    Calculate intensity metrics?:No
    Calculate thresholds?:Yes
    Use all thresholding methods?:No
    Select a thresholding method:Otsu
    Typical fraction of the image covered by objects:0.1
    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?:Background
    Select the images to measure:OrigAGP
    Include the image rescaling value?:No
    Calculate blur metrics?:No
    Spatial scale for blur measurements:20
    Calculate saturation metrics?:No
    Calculate intensity metrics?:No
    Calculate thresholds?:Yes
    Use all thresholding methods?:No
    Select a thresholding method:Otsu
    Typical fraction of the image covered by objects:0.1
    Two-class or three-class thresholding?:Three classes
    Minimize the weighted variance or the entropy?:Weighted variance
    Assign pixels in the middle intensity class to the foreground or the background?:Foreground

ExportToSpreadsheet:[module_num:4|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 column delimiter:Comma (",")
    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?: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\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?:Yes
    :
    Representation of Nan/Inf:NaN
    Add a prefix to file names?:No
    Filename prefix:AlzheimersQC_
    Overwrite existing files without warning?:No
    Data to export:Do not use
    Combine these object measurements with those of the previous object?:No
    File name:DATA.csv
    Use the object name for the file name?:Yes

CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False]
    Store batch files in default output folder?:Yes
    Output folder path:/Users/shsingh
    Are the cluster computers running Windows?:No
    Hidden\x3A in batch mode:No
    Hidden\x3A in distributed mode:No
    Hidden\x3A default input folder at time of save:/Users/shsingh/Desktop
    Hidden\x3A revision number:0
    Hidden\x3A from old matlab:No
    Launch BatchProfiler:No