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Copy pathAlignment - Batch.cppipe
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Alignment - Batch.cppipe
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CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:20140723174500
GitHash:6c2d896
ModuleCount:95
HasImagePlaneDetails:False
Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'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.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
:
Filter images?:Images only
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\'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.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Extract metadata?:No
Metadata data type:Text
Metadata types:{}
Extraction method count:1
Metadata extraction method:Extract from file/folder names
Metadata source:File name
Regular expression:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)
Regular expression:(?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 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:5|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\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\x5D
Image set matching method:Order
Set intensity range from:Image metadata
Assignments count:12
Single images count:0
Select the rule criteria:and (file does contain "One")
Name to assign these images:One
Name to assign these objects:Cell
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Two")
Name to assign these images:Two
Name to assign these objects:Nucleus
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Three")
Name to assign these images:Three
Name to assign these objects:Cytoplasm
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Four")
Name to assign these images:Four
Name to assign these objects:Speckle
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Five")
Name to assign these images:Five
Name to assign these objects:Object1
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Six")
Name to assign these images:Six
Name to assign these objects:Object2
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Seven")
Name to assign these images:Seven
Name to assign these objects:Object3
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Eight")
Name to assign these images:Eight
Name to assign these objects:Object4
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Nine")
Name to assign these images:Nine
Name to assign these objects:Object5
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Ten")
Name to assign these images:Ten
Name to assign these objects:Object6
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Eleven")
Name to assign these images:Eleven
Name to assign these objects:Object7
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "Twelve")
Name to assign these images:Twelve
Name to assign these objects:Object8
Select the image type:Color image
Set intensity range from:Image metadata
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'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.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Do you want to group your images?:No
grouping metadata count:1
Metadata category:None
IdentifyObjectsManually:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:One
Name the objects to be identified:OneObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Two
Name the objects to be identified:TwoObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Three
Name the objects to be identified:ThreeObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Four
Name the objects to be identified:FourObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Five
Name the objects to be identified:FiveObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Six
Name the objects to be identified:SixObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Seven
Name the objects to be identified:SevenObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Eight
Name the objects to be identified:EightObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Nine
Name the objects to be identified:NineObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:14|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Ten
Name the objects to be identified:TenObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:15|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Eleven
Name the objects to be identified:ElevenObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
IdentifyObjectsManually:[module_num:16|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Twelve
Name the objects to be identified:TwelveObject
Retain outlines of the identified objects?:No
Name the outlines:CellOutlines
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:One
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:AlignedFinal1
Number of digits:4
Append a suffix to the image file name?:No
Text to append to the image name:
Saved file format:tif
Output file location:Default Input Folder sub-folder\x7CPictures\\\\\\\\CP
Image bit depth:8
Overwrite existing files without warning?:No
When to save:Every 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
ConvertObjectsToImage:[module_num:18|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input objects:OneObject
Name the output image:OneImage
Select the color format:Binary (black & white)
Select the colormap:Default
ConvertObjectsToImage:[module_num:19|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input objects:TwoObject
Name the output image:TwoImage
Select the color format:Binary (black & white)
Select the colormap:Default
ColorToGray:[module_num:20|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Two
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:TwoOrigRed
Convert green to gray?:Yes
Name the output image:TwoOrigGreen
Convert blue to gray?:Yes
Name the output image:TwoOrigBlue
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:Red\x3A 1
Relative weight of the channel:1.0
Image name:Channel1
Align:[module_num:21|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the alignment method:Normalized Cross Correlation
Crop mode:Keep size
Select the first input image:OneImage
Name the first output image:OneAligned
Select the second input image:TwoImage
Name the second output image:TwoAligned
Select the additional image:TwoOrigBlue
Name the output image:TwoAlignedBlue
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigGreen
Name the output image:TwoAlignedGreen
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigRed
Name the output image:TwoAlignedRed
Select how the alignment is to be applied:Similarly
GrayToColor:[module_num:22|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 a color scheme:RGB
Select the image to be colored red:TwoAlignedRed
Select the image to be colored green:TwoAlignedGreen
Select the image to be colored blue:TwoAlignedBlue
Name the output image:TwoAlignedFinal
Relative weight for the red image:1.0
Relative weight for the green image:1.0
Relative weight for the blue image:1.0
Select the image to be colored cyan:Leave this black
Select the image to be colored magenta:Leave this black
Select the image to be colored yellow:Leave this black
Select the image that determines brightness:Leave this black
Relative weight for the cyan image:1.0
Relative weight for the magenta image:1.0
Relative weight for the yellow image:1.0
Relative weight for the brightness image:1.0
Select the input image to add to the stacked image:None
SaveImages:[module_num:23|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:TwoAlignedFinal
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:AlignedFinal2
Number of digits:4
Append a suffix to the image file name?:No
Text to append to the image name:
Saved file format:tif
Output file location:Default Input Folder sub-folder\x7CPictures\\\\\\\\CP
Image bit depth:8
Overwrite existing files without warning?:No
When to save:Every 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
ExportToSpreadsheet:[module_num:24|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 column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Limit output to a size that is allowed in Excel?:No
Select the measurements to export:Yes
Calculate the per-image mean values for object measurements?:No
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\x7C
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 to export:Image\x7CAlign_Xshift_TwoAligned,Image\x7CAlign_Yshift_TwoAligned
Representation of Nan/Inf:NaN
Add a prefix to file names?:No
Filename prefix\x3A:MyExpt_
Overwrite without warning?:No
Data to export:Image
Combine these object measurements with those of the previous object?:No
File name:Image2.csv
Use the object name for the file name?:No
ConserveMemory:[module_num:25|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Specify which images?:Images to remove
Select image to remove:TwoAligned
Select image to remove:TwoAlignedFinal
Select image to remove:TwoAlignedBlue
Select image to remove:TwoAlignedGreen
Select image to remove:TwoAlignedRed
Select image to remove:TwoImage
Select image to remove:TwoOrigGreen
Select image to remove:TwoOrigRed
Select image to remove:TwoOrigBlue
Select image to remove:Two
ConvertObjectsToImage:[module_num:26|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input objects:ThreeObject
Name the output image:TwoImage
Select the color format:Binary (black & white)
Select the colormap:Default
ColorToGray:[module_num:27|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Three
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:TwoOrigRed
Convert green to gray?:Yes
Name the output image:TwoOrigGreen
Convert blue to gray?:Yes
Name the output image:TwoOrigBlue
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:Red\x3A 1
Relative weight of the channel:1.0
Image name:Channel1
Align:[module_num:28|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the alignment method:Normalized Cross Correlation
Crop mode:Keep size
Select the first input image:OneImage
Name the first output image:OneAligned
Select the second input image:TwoImage
Name the second output image:ThreeAligned
Select the additional image:TwoOrigBlue
Name the output image:TwoAlignedBlue
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigGreen
Name the output image:TwoAlignedGreen
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigRed
Name the output image:TwoAlignedRed
Select how the alignment is to be applied:Similarly
GrayToColor:[module_num:29|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 a color scheme:RGB
Select the image to be colored red:TwoAlignedRed
Select the image to be colored green:TwoAlignedGreen
Select the image to be colored blue:TwoAlignedBlue
Name the output image:TwoAlignedFinal
Relative weight for the red image:1.0
Relative weight for the green image:1.0
Relative weight for the blue image:1.0
Select the image to be colored cyan:Leave this black
Select the image to be colored magenta:Leave this black
Select the image to be colored yellow:Leave this black
Select the image that determines brightness:Leave this black
Relative weight for the cyan image:1.0
Relative weight for the magenta image:1.0
Relative weight for the yellow image:1.0
Relative weight for the brightness image:1.0
Select the input image to add to the stacked image:None
SaveImages:[module_num:30|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:TwoAlignedFinal
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:AlignedFinal3
Number of digits:4
Append a suffix to the image file name?:No
Text to append to the image name:
Saved file format:tif
Output file location:Default Input Folder sub-folder\x7CPictures\\\\\\\\CP
Image bit depth:8
Overwrite existing files without warning?:No
When to save:Every 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
ExportToSpreadsheet:[module_num:31|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 column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Limit output to a size that is allowed in Excel?:No
Select the measurements to export:Yes
Calculate the per-image mean values for object measurements?:No
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\x7C
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 to export:Image\x7CAlign_Xshift_ThreeAligned,Image\x7CAlign_Yshift_ThreeAligned
Representation of Nan/Inf:NaN
Add a prefix to file names?:No
Filename prefix\x3A:MyExpt_
Overwrite without warning?:No
Data to export:Image
Combine these object measurements with those of the previous object?:No
File name:Image3.csv
Use the object name for the file name?:No
ConserveMemory:[module_num:32|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Specify which images?:Images to remove
Select image to remove:TwoAligned
Select image to remove:TwoAlignedFinal
Select image to remove:TwoAlignedBlue
Select image to remove:TwoAlignedGreen
Select image to remove:TwoAlignedRed
Select image to remove:TwoImage
Select image to remove:TwoOrigGreen
Select image to remove:TwoOrigRed
Select image to remove:TwoOrigBlue
Select image to remove:Two
ConvertObjectsToImage:[module_num:33|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input objects:FourObject
Name the output image:TwoImage
Select the color format:Binary (black & white)
Select the colormap:Default
ColorToGray:[module_num:34|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Four
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:TwoOrigRed
Convert green to gray?:Yes
Name the output image:TwoOrigGreen
Convert blue to gray?:Yes
Name the output image:TwoOrigBlue
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:Red\x3A 1
Relative weight of the channel:1.0
Image name:Channel1
Align:[module_num:35|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the alignment method:Normalized Cross Correlation
Crop mode:Keep size
Select the first input image:OneImage
Name the first output image:OneAligned
Select the second input image:TwoImage
Name the second output image:FourAligned
Select the additional image:TwoOrigBlue
Name the output image:TwoAlignedBlue
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigGreen
Name the output image:TwoAlignedGreen
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigRed
Name the output image:TwoAlignedRed
Select how the alignment is to be applied:Similarly
GrayToColor:[module_num:36|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 a color scheme:RGB
Select the image to be colored red:TwoAlignedRed
Select the image to be colored green:TwoAlignedGreen
Select the image to be colored blue:TwoAlignedBlue
Name the output image:TwoAlignedFinal
Relative weight for the red image:1.0
Relative weight for the green image:1.0
Relative weight for the blue image:1.0
Select the image to be colored cyan:Leave this black
Select the image to be colored magenta:Leave this black
Select the image to be colored yellow:Leave this black
Select the image that determines brightness:Leave this black
Relative weight for the cyan image:1.0
Relative weight for the magenta image:1.0
Relative weight for the yellow image:1.0
Relative weight for the brightness image:1.0
Select the input image to add to the stacked image:None
SaveImages:[module_num:37|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:TwoAlignedFinal
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:AlignedFinal4
Number of digits:4
Append a suffix to the image file name?:No
Text to append to the image name:
Saved file format:tif
Output file location:Default Input Folder sub-folder\x7CPictures\\\\\\\\CP
Image bit depth:8
Overwrite existing files without warning?:No
When to save:Every 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
ExportToSpreadsheet:[module_num:38|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 column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Limit output to a size that is allowed in Excel?:No
Select the measurements to export:Yes
Calculate the per-image mean values for object measurements?:No
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\x7C
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 to export:Image\x7CAlign_Xshift_FourAligned,Image\x7CAlign_Yshift_FourAligned
Representation of Nan/Inf:NaN
Add a prefix to file names?:No
Filename prefix\x3A:MyExpt_
Overwrite without warning?:No
Data to export:Image
Combine these object measurements with those of the previous object?:No
File name:Image4.csv
Use the object name for the file name?:No
ConserveMemory:[module_num:39|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Specify which images?:Images to remove
Select image to remove:TwoAligned
Select image to remove:TwoAlignedFinal
Select image to remove:TwoAlignedBlue
Select image to remove:TwoAlignedGreen
Select image to remove:TwoAlignedRed
Select image to remove:TwoImage
Select image to remove:TwoOrigGreen
Select image to remove:TwoOrigRed
Select image to remove:TwoOrigBlue
Select image to remove:Two
ConvertObjectsToImage:[module_num:40|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input objects:FiveObject
Name the output image:TwoImage
Select the color format:Binary (black & white)
Select the colormap:Default
ColorToGray:[module_num:41|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Five
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:TwoOrigRed
Convert green to gray?:Yes
Name the output image:TwoOrigGreen
Convert blue to gray?:Yes
Name the output image:TwoOrigBlue
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:Red\x3A 1
Relative weight of the channel:1.0
Image name:Channel1
Align:[module_num:42|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the alignment method:Normalized Cross Correlation
Crop mode:Keep size
Select the first input image:OneImage
Name the first output image:OneAligned
Select the second input image:TwoImage
Name the second output image:FiveAligned
Select the additional image:TwoOrigBlue
Name the output image:TwoAlignedBlue
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigGreen
Name the output image:TwoAlignedGreen
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigRed
Name the output image:TwoAlignedRed
Select how the alignment is to be applied:Similarly
GrayToColor:[module_num:43|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 a color scheme:RGB
Select the image to be colored red:TwoAlignedRed
Select the image to be colored green:TwoAlignedGreen
Select the image to be colored blue:TwoAlignedBlue
Name the output image:TwoAlignedFinal
Relative weight for the red image:1.0
Relative weight for the green image:1.0
Relative weight for the blue image:1.0
Select the image to be colored cyan:Leave this black
Select the image to be colored magenta:Leave this black
Select the image to be colored yellow:Leave this black
Select the image that determines brightness:Leave this black
Relative weight for the cyan image:1.0
Relative weight for the magenta image:1.0
Relative weight for the yellow image:1.0
Relative weight for the brightness image:1.0
Select the input image to add to the stacked image:None
SaveImages:[module_num:44|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:TwoAlignedFinal
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:AlignedFinal5
Number of digits:4
Append a suffix to the image file name?:No
Text to append to the image name:
Saved file format:tif
Output file location:Default Input Folder sub-folder\x7CPictures\\\\\\\\CP
Image bit depth:8
Overwrite existing files without warning?:No
When to save:Every 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
ExportToSpreadsheet:[module_num:45|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 column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Limit output to a size that is allowed in Excel?:No
Select the measurements to export:Yes
Calculate the per-image mean values for object measurements?:No
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\x7C
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 to export:Image\x7CAlign_Xshift_FiveAligned,Image\x7CAlign_Yshift_FiveAligned
Representation of Nan/Inf:NaN
Add a prefix to file names?:No
Filename prefix\x3A:MyExpt_
Overwrite without warning?:No
Data to export:Image
Combine these object measurements with those of the previous object?:No
File name:Image5.csv
Use the object name for the file name?:No
ConserveMemory:[module_num:46|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Specify which images?:Images to remove
Select image to remove:TwoAligned
Select image to remove:TwoAlignedFinal
Select image to remove:TwoAlignedBlue
Select image to remove:TwoAlignedGreen
Select image to remove:TwoAlignedRed
Select image to remove:TwoImage
Select image to remove:TwoOrigGreen
Select image to remove:TwoOrigRed
Select image to remove:TwoOrigBlue
Select image to remove:Two
ConvertObjectsToImage:[module_num:47|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input objects:SixObject
Name the output image:TwoImage
Select the color format:Binary (black & white)
Select the colormap:Default
ColorToGray:[module_num:48|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Six
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:TwoOrigRed
Convert green to gray?:Yes
Name the output image:TwoOrigGreen
Convert blue to gray?:Yes
Name the output image:TwoOrigBlue
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:Red\x3A 1
Relative weight of the channel:1.0
Image name:Channel1
Align:[module_num:49|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the alignment method:Normalized Cross Correlation
Crop mode:Keep size
Select the first input image:OneImage
Name the first output image:OneAligned
Select the second input image:TwoImage
Name the second output image:SixAligned
Select the additional image:TwoOrigBlue
Name the output image:TwoAlignedBlue
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigGreen
Name the output image:TwoAlignedGreen
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigRed
Name the output image:TwoAlignedRed
Select how the alignment is to be applied:Similarly
GrayToColor:[module_num:50|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 a color scheme:RGB
Select the image to be colored red:TwoAlignedRed
Select the image to be colored green:TwoAlignedGreen
Select the image to be colored blue:TwoAlignedBlue
Name the output image:TwoAlignedFinal
Relative weight for the red image:1.0
Relative weight for the green image:1.0
Relative weight for the blue image:1.0
Select the image to be colored cyan:Leave this black
Select the image to be colored magenta:Leave this black
Select the image to be colored yellow:Leave this black
Select the image that determines brightness:Leave this black
Relative weight for the cyan image:1.0
Relative weight for the magenta image:1.0
Relative weight for the yellow image:1.0
Relative weight for the brightness image:1.0
Select the input image to add to the stacked image:None
SaveImages:[module_num:51|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:TwoAlignedFinal
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:AlignedFinal6
Number of digits:4
Append a suffix to the image file name?:No
Text to append to the image name:
Saved file format:tif
Output file location:Default Input Folder sub-folder\x7CPictures\\\\\\\\CP
Image bit depth:8
Overwrite existing files without warning?:No
When to save:Every 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
ExportToSpreadsheet:[module_num:52|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 column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Limit output to a size that is allowed in Excel?:No
Select the measurements to export:Yes
Calculate the per-image mean values for object measurements?:No
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\x7C
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 to export:Image\x7CAlign_Xshift_SixAligned,Image\x7CAlign_Yshift_SixAligned
Representation of Nan/Inf:NaN
Add a prefix to file names?:No
Filename prefix\x3A:MyExpt_
Overwrite without warning?:No
Data to export:Image
Combine these object measurements with those of the previous object?:No
File name:Image6.csv
Use the object name for the file name?:No
ConserveMemory:[module_num:53|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Specify which images?:Images to remove
Select image to remove:TwoAligned
Select image to remove:TwoAlignedFinal
Select image to remove:TwoAlignedBlue
Select image to remove:TwoAlignedGreen
Select image to remove:TwoAlignedRed
Select image to remove:TwoImage
Select image to remove:TwoOrigGreen
Select image to remove:TwoOrigRed
Select image to remove:TwoOrigBlue
Select image to remove:Two
ConvertObjectsToImage:[module_num:54|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input objects:SevenObject
Name the output image:TwoImage
Select the color format:Binary (black & white)
Select the colormap:Default
ColorToGray:[module_num:55|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:Seven
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:TwoOrigRed
Convert green to gray?:Yes
Name the output image:TwoOrigGreen
Convert blue to gray?:Yes
Name the output image:TwoOrigBlue
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:Red\x3A 1
Relative weight of the channel:1.0
Image name:Channel1
Align:[module_num:56|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the alignment method:Normalized Cross Correlation
Crop mode:Keep size
Select the first input image:OneImage
Name the first output image:OneAligned
Select the second input image:TwoImage
Name the second output image:SevenAligned
Select the additional image:TwoOrigBlue
Name the output image:TwoAlignedBlue
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigGreen
Name the output image:TwoAlignedGreen
Select how the alignment is to be applied:Similarly
Select the additional image:TwoOrigRed
Name the output image:TwoAlignedRed
Select how the alignment is to be applied:Similarly
GrayToColor:[module_num:57|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 a color scheme:RGB
Select the image to be colored red:TwoAlignedRed
Select the image to be colored green:TwoAlignedGreen
Select the image to be colored blue:TwoAlignedBlue
Name the output image:TwoAlignedFinal
Relative weight for the red image:1.0
Relative weight for the green image:1.0
Relative weight for the blue image:1.0
Select the image to be colored cyan:Leave this black
Select the image to be colored magenta:Leave this black
Select the image to be colored yellow:Leave this black
Select the image that determines brightness:Leave this black
Relative weight for the cyan image:1.0
Relative weight for the magenta image:1.0
Relative weight for the yellow image:1.0
Relative weight for the brightness image:1.0
Select the input image to add to the stacked image:None
SaveImages:[module_num:58|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:TwoAlignedFinal
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:AlignedFinal7
Number of digits:4
Append a suffix to the image file name?:No
Text to append to the image name:
Saved file format:tif
Output file location:Default Input Folder sub-folder\x7CPictures\\\\\\\\CP
Image bit depth:8
Overwrite existing files without warning?:No
When to save:Every 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
ExportToSpreadsheet:[module_num:59|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 column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Limit output to a size that is allowed in Excel?:No
Select the measurements to export:Yes
Calculate the per-image mean values for object measurements?:No
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\x7C
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 to export:Image\x7CAlign_Xshift_SevenAligned,Image\x7CAlign_Yshift_SevenAligned
Representation of Nan/Inf:NaN
Add a prefix to file names?:No
Filename prefix\x3A:MyExpt_
Overwrite without warning?:No
Data to export:Image
Combine these object measurements with those of the previous object?:No
File name:Image7.csv
Use the object name for the file name?:No
ConserveMemory:[module_num:60|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Specify which images?:Images to remove
Select image to remove:TwoAligned
Select image to remove:TwoAlignedFinal
Select image to remove:TwoAlignedBlue
Select image to remove:TwoAlignedGreen
Select image to remove:TwoAlignedRed
Select image to remove:TwoImage
Select image to remove:TwoOrigGreen
Select image to remove:TwoOrigRed
Select image to remove:TwoOrigBlue
Select image to remove:Two
ConvertObjectsToImage:[module_num:61|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input objects:EightObject
Name the output image:TwoImage
Select the color format:Binary (black & white)