chlamy_segment.cppipe

CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:425
GitHash:
ModuleCount:10
HasImagePlaneDetails:False

Images:[module_num:1|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:['To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    :
    Filter images?:No filtering
    Select the rule criteria:and (file does contain "cr_w_pools")

Metadata:[module_num:2|svn_version:'Unknown'|variable_revision_number:6|show_window:False|notes:['The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Extract metadata?:Yes
    Metadata data type:Choose for each
    Metadata types:{}
    Extraction method count:1
    Metadata extraction method:Extract from file/folder names
    Metadata source:File name
    Regular expression to extract from file name:^(?P<species>.*)_pools_slide1_(?P<poolid>.*)_Probabilities
    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
    Extract metadata from:All images
    Select the filtering criteria:and (file does contain "")
    Metadata file location:Elsewhere...|
    Match file and image metadata:[]
    Use case insensitive matching?:No
    Metadata file name:None
    Does cached metadata exist?:No

NamesAndTypes:[module_num:3|svn_version:'Unknown'|variable_revision_number:8|show_window:False|notes:['The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Assign a name to:All images
    Select the image type:Color image
    Name to assign these images:pool
    Match metadata:[]
    Image set matching method:Order
    Set intensity range from:Image bit-depth
    Assignments count:1
    Single images count:0
    Maximum intensity:255.0
    Process as 3D?:No
    Relative pixel spacing in X:1.0
    Relative pixel spacing in Y:1.0
    Relative pixel spacing in Z:1.0
    Select the rule criteria:and (file does contain "")
    Name to assign these images:DNA
    Name to assign these objects:Cell
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Maximum intensity:255.0

Groups:[module_num:4|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:['The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Do you want to group your images?:Yes
    grouping metadata count:2
    Metadata category:species
    Metadata category:poolid

ColorToGray:[module_num:5|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:pool
    Conversion method:Split
    Image type:RGB
    Name the output image:OrigGray
    Relative weight of the red channel:1.0
    Relative weight of the green channel:1.0
    Relative weight of the blue channel:1.0
    Convert red to gray?:Yes
    Name the output image:chlamy_prob
    Convert green to gray?:No
    Name the output image:OrigGreen
    Convert blue to gray?:No
    Name the output image:OrigBlue
    Convert hue to gray?:Yes
    Name the output image:OrigHue
    Convert saturation to gray?:Yes
    Name the output image:OrigSaturation
    Convert value to gray?:Yes
    Name the output image:OrigValue
    Channel count:1
    Channel number:1
    Relative weight of the channel:1.0
    Image name:Channel1

IdentifyPrimaryObjects:[module_num:6|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:chlamy_prob
    Name the primary objects to be identified:chlamy
    Typical diameter of objects, in pixel units (Min,Max):5,40
    Discard objects outside the diameter range?:Yes
    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:25
    Suppress local maxima that are closer than this minimum allowed distance:25
    Speed up by using lower-resolution image to find local maxima?:Yes
    Fill holes in identified objects?:After both thresholding and declumping
    Automatically calculate size of smoothing filter for declumping?:No
    Automatically calculate minimum allowed distance between local maxima?:No
    Handling of objects if excessive number of objects identified:Continue
    Maximum number of objects:500
    Use advanced settings?:Yes
    Threshold setting version:12
    Threshold strategy:Global
    Thresholding method:Manual
    Threshold smoothing scale:1.3488
    Threshold correction factor:1.0
    Lower and upper bounds on threshold:0.0,1.0
    Manual threshold:0.5
    Select the measurement to threshold with:None
    Two-class or three-class thresholding?:Two classes
    Log transform before thresholding?:No
    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
    Size of adaptive window:50
    Lower outlier fraction:0.05
    Upper outlier fraction:0.05
    Averaging method:Mean
    Variance method:Standard deviation
    # of deviations:2.0
    Thresholding method:Minimum Cross-Entropy

MeasureObjectSizeShape:[module_num:7|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select object sets to measure:chlamy
    Calculate the Zernike features?:Yes
    Calculate the advanced features?:Yes

ConvertObjectsToImage:[module_num:8|svn_version:'Unknown'|variable_revision_number:1|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input objects:chlamy
    Name the output image:chlamy_img
    Select the color format:Binary (black & white)
    Select the colormap:Default

SaveImages:[module_num:9|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:chlamy_img
    Select method for constructing file names:From image filename
    Select image name for file prefix:pool
    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:_obj
    Saved file format:tiff
    Output file location:Default Output Folder sub-folder|images
    Image bit depth:8-bit integer
    Overwrite existing files without warning?:No
    When to save:Every cycle
    Record the file and path information to the saved image?:No
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...|
    How to save the series:T (Time)
    Save with lossless compression?:Yes

ExportToSpreadsheet:[module_num:10|svn_version:'Unknown'|variable_revision_number:13|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the column delimiter:Comma (",")
    Add image metadata columns to your object data file?:No
    Add image file and folder names to your object data file?: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?:No
    Calculate the per-image standard deviation values for object measurements?:Yes
    Output file location:Default Output Folder sub-folder|data
    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
    Press button to select measurements:
    Representation of Nan/Inf:NaN
    Add a prefix to file names?:Yes
    Filename prefix:chlamy_obj
    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