ExampleTrackObjects.cppipe

CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:400
GitHash:
ModuleCount:13
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?:Images only
    Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "[\\\\\\\\/]\\\\.")

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.', 'â\x80\x94', 'Use regular expressions to match and name metadata in the file and path names. ']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Extract metadata?:Yes
    Metadata data type:Text
    Metadata types:{}
    Extraction method count:2
    Metadata extraction method:Extract from file/folder names
    Metadata source:File name
    Regular expression to extract from file name:^(?P<Specimen>.*)_(?P<Stain>.*)_(?P<FrameNumber>[0-9]*)
    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
    Extract metadata from:Images matching a rule
    Select the filtering criteria:and (file does containregexp "GFPHistone")
    Metadata file location:Elsewhere...|
    Match file and image metadata:[]
    Use case insensitive matching?:No
    Metadata file name:
    Does cached metadata exist?:No
    Metadata extraction method:Extract from file/folder names
    Metadata source:Folder name
    Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>[A-P][0-9]{2})_s(?P<Site>[0-9])_w(?P<ChannelNumber>[0-9])
    Regular expression to extract from folder name:.*[\\\\/](?P<Run>.*)$
    Extract metadata from:Images matching a rule
    Select the filtering criteria:and (file does containregexp "GFPHistone")
    Metadata file location:Elsewhere...|
    Match file and image metadata:[]
    Use case insensitive matching?:No
    Metadata file name:
    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.', 'â\x80\x94', 'Load the images by matching files in all folders against the text pattern â\x80\x98GFPHistoneâ\x80\x99.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Assign a name to:Images matching rules
    Select the image type:Grayscale image
    Name to assign these images:DNA
    Match metadata:[]
    Image set matching method:Order
    Set intensity range from:Image metadata
    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 containregexp "GFPHistone")
    Name to assign these images:OrigColor
    Name to assign these objects:Cell
    Select the image type:Color 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.', 'â\x80\x94', 'Group the analysis by the â\x80\x98Runâ\x80\x99 metadata so that each folder is analyzed separately. ']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Do you want to group your images?:Yes
    grouping metadata count:1
    Metadata category:Run

ColorToGray:[module_num:5|svn_version:'Unknown'|variable_revision_number:4|show_window:True|notes:['Convert the color image to grayscale.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:OrigColor
    Conversion method:Combine
    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:OrigRed
    Convert green to gray?:Yes
    Name the output image:OrigGreen
    Convert blue to gray?:Yes
    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:14|show_window:True|notes:['Identify the fly embryos from the histone stain image. Three-class thresholding works better than the default two-class method.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:OrigGray
    Name the primary objects to be identified:Embryos
    Typical diameter of objects, in pixel units (Min,Max):25,9999
    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:10
    Suppress local maxima that are closer than this minimum allowed distance:7.0
    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?:Yes
    Automatically calculate minimum allowed distance between local maxima?:Yes
    Handling of objects if excessive number of objects identified:Continue
    Maximum number of objects:500
    Display accepted local maxima?:No
    Select maxima color:Blue
    Use advanced settings?:Yes
    Threshold setting version:11
    Threshold strategy:Global
    Thresholding method:Otsu
    Threshold smoothing scale:1.3488
    Threshold correction factor:1
    Lower and upper bounds on threshold:0.01,1.0
    Manual threshold:0.0
    Select the measurement to threshold with:None
    Two-class or three-class thresholding?:Two classes
    Assign pixels in the middle intensity class to the foreground or the background?:Background
    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:Otsu

MeasureObjectSizeShape:[module_num:7|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:['Measure the morphology of each embryo.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select object sets to measure:Embryos
    Calculate the Zernike features?:No
    Calculate the advanced features?:No

MeasureObjectIntensity:[module_num:8|svn_version:'Unknown'|variable_revision_number:4|show_window:True|notes:['Measure the grayscale intensity of each embryo.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select images to measure:OrigGray
    Select objects to measure:Embryos

TrackObjects:[module_num:9|svn_version:'Unknown'|variable_revision_number:7|show_window:True|notes:['Track the embryos across images using the Overlap method: tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Choose a tracking method:Overlap
    Select the objects to track:Embryos
    Select object measurement to use for tracking:None
    Maximum pixel distance to consider matches:50
    Select display option:Color and Number
    Save color-coded image?:Yes
    Name the output image:TrackedCells
    Select the movement model:Both
    Number of standard deviations for search radius:3.0
    Search radius limit, in pixel units (Min,Max):2.0,10.0
    Run the second phase of the LAP algorithm?:Yes
    Gap closing cost:40
    Split alternative cost:40
    Merge alternative cost:40
    Maximum gap displacement, in pixel units:5
    Maximum split score:50
    Maximum merge score:50
    Maximum temporal gap, in frames:5
    Filter objects by lifetime?:No
    Filter using a minimum lifetime?:Yes
    Minimum lifetime:1
    Filter using a maximum lifetime?:No
    Maximum lifetime:100
    Mitosis alternative cost:80
    Maximum mitosis distance, in pixel units:40
    Average cell diameter in pixels:35.0
    Use advanced configuration parameters:No
    Cost of cell to empty matching:15.0
    Weight of area difference in function matching cost:25.0

OverlayOutlines:[module_num:10|svn_version:'Unknown'|variable_revision_number:4|show_window:True|notes:['Overlay the embryo outlines on the grayscale image.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Display outlines on a blank image?:No
    Select image on which to display outlines:OrigGray
    Name the output image:OutlineImage
    Outline display mode:Color
    Select method to determine brightness of outlines:Max of image
    How to outline:Inner
    Select outline color:Red
    Select objects to display:Embryos

Tile:[module_num:11|svn_version:'Unknown'|variable_revision_number:1|show_window:True|notes:['Tile the original color image, the outlined image and the image of tracked labels together.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select an input image:OrigColor
    Name the output image:AdjacentImage
    Tile assembly method:Within cycles
    Final number of rows:1
    Final number of columns:12
    Image corner to begin tiling:top left
    Direction to begin tiling:row
    Use meander mode?:No
    Automatically calculate number of rows?:No
    Automatically calculate number of columns?:Yes
    Select an additional image to tile:OutlineImage
    Select an additional image to tile:TrackedCells

SaveImages:[module_num:12|svn_version:'Unknown'|variable_revision_number:15|show_window:True|notes:['Save the tiled image as an PNG, naming each image according to â\x80\x98Specimenâ\x80\x99 and â\x80\x98Frameâ\x80\x99 metadata of the original image. Save the image in a new sub-folder created and named according to the â\x80\x98Runâ\x80\x99 metadata.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:AdjacentImage
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\g<Specimen>-\g<FrameNumber>
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:png
    Output file location:Default Output Folder sub-folder|\g<Run>
    Image bit depth:8-bit integer
    Overwrite existing files without warning?:Yes
    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)

ExportToSpreadsheet:[module_num:13|svn_version:'Unknown'|variable_revision_number:13|show_window:True|notes:['Export any measurements to a comma-delimited file (.csv). The measurements made for the embryo objects will be saved to separate .csv files, in addition to the per-image .csv.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the column delimiter:Comma (",")
    Add image metadata columns to your object data file?:Yes
    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?:No
    Output file location:Default Output Folder sub-folder|\g<Run>
    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
    Press button to select measurements:
    Representation of Nan/Inf:NaN
    Add a prefix to file names?:No
    Filename prefix:MyExpt_
    Overwrite existing files without warning?:Yes
    Data to export:Image
    Combine these object measurements with those of the previous object?:No
    File name:DATA.csv
    Use the object name for the file name?:Yes
    Data to export:Embryos
    Combine these object measurements with those of the previous object?:No
    File name:DATA.csv
    Use the object name for the file name?:Yes