test_deepprofiler.cppipe

CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:425
GitHash:
ModuleCount:6
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.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Extract metadata?:Yes
    Metadata data type:Text
    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<Well>.*)_.*_.*_(?P<Site>.*)_(?P<Channel>.*)_001.tif
    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: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:5
    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 "DAPI")
    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
    Select the rule criteria:and (file does contain "GFP")
    Name to assign these images:ER
    Name to assign these objects:Nucleus
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Maximum intensity:255.0
    Select the rule criteria:and (file does contain "Propidium")
    Name to assign these images:AGP
    Name to assign these objects:Cytoplasm
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Maximum intensity:255.0
    Select the rule criteria:and (file does contain "CY5")
    Name to assign these images:Mito
    Name to assign these objects:Speckle
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Maximum intensity:255.0
    Select the rule criteria:and (file does contain "CY5")
    Name to assign these images:RNA
    Name to assign these objects:Object1
    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?:No
    grouping metadata count:1
    Metadata category:None

IdentifyPrimaryObjects:[module_num:5|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:DNA
    Name the primary objects to be identified:IdentifyPrimaryObjects
    Typical diameter of objects, in pixel units (Min,Max):30,200
    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
    Use advanced settings?:Yes
    Threshold setting version:12
    Threshold strategy:Global
    Thresholding method:Otsu
    Threshold smoothing scale:1.3488
    Threshold correction factor:1.0
    Lower and upper bounds on threshold:0.0,1.0
    Manual threshold:0.0
    Select the measurement to threshold with:None
    Two-class or three-class thresholding?:Three classes
    Log transform before thresholding?:No
    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:Minimum Cross-Entropy

RunDeepProfiler:[module_num:6|svn_version:'Unknown'|variable_revision_number:1|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select images to measure:AGP, DNA, ER, Mito, RNA
    Input nuclei object name:IdentifyPrimaryObjects
    Name this experiment.:FeaturesDeepProfiler
    Output file location:Elsewhere...|C:\\Users\\fossa\\Desktop\\deepprofiler\\example\\run
    DeepProfiler directory:Elsewhere...|C:\Users\fossa\DeepProfiler
    Model directory:Elsewhere...|C:\Users\fossa\Desktop\deepprofiler\example
    Model file:Cell_Painting_CNN_v1.hdf5
    Select Metadata_Plate:Metadata_Frame
    Select Metadata_Well:Metadata_Well
    Select Metadata_Site:Metadata_Site
    Config directory:Elsewhere...|C:\\Users\\fossa\\Desktop\\deepprofiler\\example
    Model file:profiling.json