illum.cppipe

CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:20160418141927
GitHash:9969f42
ModuleCount:18
HasImagePlaneDetails:False

LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|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
    Rescale intensities?:Yes

Resize:[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]
    Select the input image:OrigDNA
    Name the output image:DownsampledDNA
    Resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:0.1
    Width of the final image:100
    Height of the final image:100
    Interpolation method:Bilinear
    Method to specify the dimensions:Manual
    Select the image with the desired dimensions:None
    Additional image count:0

CorrectIlluminationCalculate:[module_num:3|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:DownsampledDNA
    Name the output image:IllumDNA
    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:Median Filter
    Method to calculate smoothing filter size:Manually
    Approximate object size:10
    Smoothing filter size:20
    Retain the averaged image?:No
    Name the averaged image:IllumBlueAvg
    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

Resize:[module_num:4|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]
    Select the input image:IllumDNA
    Name the output image:UpsampledIllumDNA
    Resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:10
    Width of the final image:100
    Height of the final image:100
    Interpolation method:Bilinear
    Method to specify the dimensions:Manual
    Select the image with the desired dimensions:None
    Additional image count:0

Resize:[module_num:5|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]
    Select the input image:OrigER_RNA
    Name the output image:DownsampledER_RNA
    Resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:0.1
    Width of the final image:100
    Height of the final image:100
    Interpolation method:Bilinear
    Method to specify the dimensions:Manual
    Select the image with the desired dimensions:None
    Additional image count:0

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:DownsampledER_RNA
    Name the output image:IllumER_RNA
    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:Median Filter
    Method to calculate smoothing filter size:Manually
    Approximate object size:10
    Smoothing filter size:20
    Retain the averaged image?:No
    Name the averaged image:IllumBlueAvg
    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

Resize:[module_num:7|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]
    Select the input image:IllumER_RNA
    Name the output image:UpsampledIllumER_RNA
    Resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:10
    Width of the final image:100
    Height of the final image:100
    Interpolation method:Bilinear
    Method to specify the dimensions:Manual
    Select the image with the desired dimensions:None
    Additional image count:0

Resize:[module_num:8|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]
    Select the input image:OrigAGP
    Name the output image:DownsampledAGP
    Resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:0.1
    Width of the final image:100
    Height of the final image:100
    Interpolation method:Bilinear
    Method to specify the dimensions:Manual
    Select the image with the desired dimensions:None
    Additional image count:0

CorrectIlluminationCalculate:[module_num:9|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:DownsampledAGP
    Name the output image:IllumAGP
    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:Median Filter
    Method to calculate smoothing filter size:Manually
    Approximate object size:10
    Smoothing filter size:20
    Retain the averaged image?:No
    Name the averaged image:IllumBlueAvg
    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

Resize:[module_num:10|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]
    Select the input image:IllumAGP
    Name the output image:UpsampledIllumAGP
    Resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:10
    Width of the final image:100
    Height of the final image:100
    Interpolation method:Bilinear
    Method to specify the dimensions:Manual
    Select the image with the desired dimensions:None
    Additional image count:0

Resize:[module_num:11|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]
    Select the input image:OrigMito
    Name the output image:DownsampledMito
    Resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:0.1
    Width of the final image:100
    Height of the final image:100
    Interpolation method:Bilinear
    Method to specify the dimensions:Manual
    Select the image with the desired dimensions:None
    Additional image count:0

CorrectIlluminationCalculate:[module_num:12|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:DownsampledMito
    Name the output image:IllumMito
    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:Median Filter
    Method to calculate smoothing filter size:Manually
    Approximate object size:10
    Smoothing filter size:20
    Retain the averaged image?:No
    Name the averaged image:IllumBlueAvg
    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

Resize:[module_num:13|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]
    Select the input image:IllumMito
    Name the output image:UpsampledIllumMito
    Resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:10
    Width of the final image:100
    Height of the final image:100
    Interpolation method:Bilinear
    Method to specify the dimensions:Manual
    Select the image with the desired dimensions:None
    Additional image count:0

SaveImages:[module_num:14|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 type of image to save:Image
    Select the image to save:UpsampledIllumDNA
    Select the objects to save:None
    Select the module display window to save:None
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<Plate>_IllumDNA
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:mat
    Output file location:Default Output Folder\x7C
    Image bit depth:16-bit integer
    Overwrite existing files without warning?:No
    When to save:Last cycle
    Rescale the images? :No
    Save as grayscale or color image?:Grayscale
    Select colormap:gray
    Record the file and path information to the saved image?:No
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C
    Saved movie format:avi

SaveImages:[module_num:15|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 type of image to save:Image
    Select the image to save:UpsampledIllumER_RNA
    Select the objects to save:None
    Select the module display window to save:None
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<Plate>_IllumER_RNA
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:mat
    Output file location:Default Output Folder\x7C
    Image bit depth:16-bit integer
    Overwrite existing files without warning?:No
    When to save:Last cycle
    Rescale the images? :No
    Save as grayscale or color image?:Grayscale
    Select colormap:gray
    Record the file and path information to the saved image?:No
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C
    Saved movie format:avi

SaveImages:[module_num:16|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 type of image to save:Image
    Select the image to save:UpsampledIllumMito
    Select the objects to save:None
    Select the module display window to save:None
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<Plate>_IllumMito
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:mat
    Output file location:Default Output Folder\x7C
    Image bit depth:16-bit integer
    Overwrite existing files without warning?:No
    When to save:Last cycle
    Rescale the images? :No
    Save as grayscale or color image?:Grayscale
    Select colormap:gray
    Record the file and path information to the saved image?:No
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C
    Saved movie format:avi

SaveImages:[module_num:17|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 type of image to save:Image
    Select the image to save:UpsampledIllumAGP
    Select the objects to save:None
    Select the module display window to save:None
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<Plate>_IllumAGP
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:mat
    Output file location:Default Output Folder\x7C
    Image bit depth:16-bit integer
    Overwrite existing files without warning?:No
    When to save:Last cycle
    Rescale the images? :No
    Save as grayscale or color image?:Grayscale
    Select colormap:gray
    Record the file and path information to the saved image?:No
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C
    Saved movie format:avi

CreateBatchFiles:[module_num:18|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|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