CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:300
GitHash:
ModuleCount:13
HasImagePlaneDetails:False

Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    :
    Filter images?:No filtering
    Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\x5B\\\\\\\\\\\\\\\\/\x5D\\\\\\\\.")

Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'\'\x5D|batch_state:array(\x5B\x5D, 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<well>\x5BA-Z\x5D\\\\d+)_s(?P<site>\\\\d+)_w(?P<channel>\\\\d).*\\\\.tif
    Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$
    Extract metadata from:All images
    Select the filtering criteria:and (file does containregexp "^(?P<Plate>.+?)\\\\\\\\_IllumDAPI\\\\\\\\.mat$")
    Metadata file location:
    Match file and image metadata:\x5B\x5D
    Use case insensitive matching?:No
    Metadata extraction method:Extract from file/folder names
    Metadata source:Folder name
    Regular expression to extract from file name:.*(\\\\\\\\\x7C/)(?P<folder>.*)(\\\\\\\\\x7C/)
    Regular expression to extract from folder name:.*(\\\\\\\\\x7C/)(?P<folder>.*)
    Extract metadata from:All images
    Select the filtering criteria:and (file does contain "")
    Metadata file location:
    Match file and image metadata:\x5B\x5D
    Use case insensitive matching?:No

NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'\'\x5D|batch_state:array(\x5B\x5D, 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:\x5B{u\'DAPI\'\x3A u\'folder\', u\'Tubulin\'\x3A u\'folder\', u\'Actin\'\x3A u\'folder\'}, {u\'Tubulin\'\x3A u\'well\', u\'DAPI\'\x3A u\'well\', u\'Actin\'\x3A u\'well\'}, {u\'Tubulin\'\x3A u\'site\', u\'DAPI\'\x3A u\'site\', u\'Actin\'\x3A u\'site\'}\x5D
    Image set matching method:Metadata
    Set intensity range from:Image metadata
    Assignments count:3
    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 (metadata does channel "1")
    Name to assign these images:DAPI
    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 (metadata does channel "2")
    Name to assign these images:Actin
    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 (metadata does channel "4")
    Name to assign these images:Tubulin
    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:\x5B\'\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Do you want to group your images?:Yes
    grouping metadata count:1
    Metadata category:folder

CorrectIlluminationCalculate:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:DAPI
    Name the output image:IllumDAPI
    Select how the illumination function is calculated:Regular
    Dilate objects in the final averaged image?:No
    Dilation radius:1
    Block size:60
    Rescale the illumination function?:Yes
    Calculate function for each image individually, or based on all images?:All\x3A Across cycles
    Smoothing method:Gaussian Filter
    Method to calculate smoothing filter size:Manually
    Approximate object diameter:10
    Smoothing filter size:500
    Retain the averaged image?:Yes
    Name the averaged image:IllumDAPIAvg
    Retain the dilated image?:No
    Name the dilated image:IllumBlueDilated
    Automatically calculate spline parameters?:Yes
    Background mode:auto
    Number of spline points:5
    Background threshold:2.0
    Image resampling factor:2.0
    Maximum number of iterations:40
    Residual value for convergence:0.001

CorrectIlluminationCalculate:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:Actin
    Name the output image:IllumActin
    Select how the illumination function is calculated:Regular
    Dilate objects in the final averaged image?:No
    Dilation radius:1
    Block size:60
    Rescale the illumination function?:Yes
    Calculate function for each image individually, or based on all images?:All\x3A Across cycles
    Smoothing method:Gaussian Filter
    Method to calculate smoothing filter size:Manually
    Approximate object diameter:10
    Smoothing filter size:500
    Retain the averaged image?:Yes
    Name the averaged image:IllumActinAvg
    Retain the dilated image?:No
    Name the dilated image:IllumBlueDilated
    Automatically calculate spline parameters?:Yes
    Background mode:auto
    Number of spline points:5
    Background threshold:2.0
    Image resampling factor:2.0
    Maximum number of iterations:40
    Residual value for convergence:0.001

CorrectIlluminationCalculate:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:Tubulin
    Name the output image:IllumTubulin
    Select how the illumination function is calculated:Regular
    Dilate objects in the final averaged image?:No
    Dilation radius:1
    Block size:60
    Rescale the illumination function?:Yes
    Calculate function for each image individually, or based on all images?:All\x3A Across cycles
    Smoothing method:Gaussian Filter
    Method to calculate smoothing filter size:Manually
    Approximate object diameter:10
    Smoothing filter size:500
    Retain the averaged image?:Yes
    Name the averaged image:IllumTubulinAvg
    Retain the dilated image?:No
    Name the dilated image:IllumBlueDilated
    Automatically calculate spline parameters?:Yes
    Background mode:auto
    Number of spline points:5
    Background threshold:2.0
    Image resampling factor:2.0
    Maximum number of iterations:40
    Residual value for convergence:0.001

SaveImages:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:IllumActin
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<folder>_IllumActin
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:npy
    Output file location:Default Output Folder\x7C
    Image bit depth:32-bit floating point
    Overwrite existing files without warning?:Yes
    When to save:Last cycle
    Record the file and path information to the saved image?:Yes
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C

SaveImages:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:IllumDAPI
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<folder>_IllumDAPI
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:npy
    Output file location:Default Output Folder\x7C
    Image bit depth:32-bit floating point
    Overwrite existing files without warning?:Yes
    When to save:Last cycle
    Record the file and path information to the saved image?:Yes
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C

SaveImages:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:IllumTubulin
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<folder>_IllumTubulin
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:npy
    Output file location:Default Output Folder\x7C
    Image bit depth:32-bit floating point
    Overwrite existing files without warning?:Yes
    When to save:Last cycle
    Record the file and path information to the saved image?:Yes
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C

SaveImages:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:IllumActinAvg
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<folder>_IllumActinAvg
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:npy
    Output file location:Default Output Folder\x7C
    Image bit depth:32-bit floating point
    Overwrite existing files without warning?:Yes
    When to save:Last cycle
    Record the file and path information to the saved image?:Yes
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C

SaveImages:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:IllumDAPIAvg
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<folder>_IllumDAPIAvg
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:npy
    Output file location:Default Output Folder\x7C
    Image bit depth:32-bit floating point
    Overwrite existing files without warning?:Yes
    When to save:Last cycle
    Record the file and path information to the saved image?:Yes
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C

SaveImages:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:IllumTubulinAvg
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<folder>_IllumTubulinAvg
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:npy
    Output file location:Default Output Folder\x7C
    Image bit depth:32-bit floating point
    Overwrite existing files without warning?:Yes
    When to save:Last cycle
    Record the file and path information to the saved image?:Yes
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C