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3channels.cppipe
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CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:20140723174500
GitHash:6c2d896
ModuleCount:8
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.\', \'---\', \'Settings converted from legacy pipeline.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
:
Filter images?:Custom
Select the rule criteria:and (extension does isimage) (file doesnot contain "Thumb")
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.\', \'---\', \'Settings converted from legacy pipeline.\'\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: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:or (file does contain "w1")
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.\', \'---\', \'Settings converted from legacy pipeline.\', \'Please change any color images from "Load as Grayscale image" to "Load as Color image"\'\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\'Plate\', u\'TRITC\'\x3A None, u\'TL\'\x3A u\'Plate\', u\'GFP\'\x3A u\'Plate\'}, {u\'DAPI\'\x3A u\'Well\', u\'TRITC\'\x3A None, u\'TL\'\x3A u\'Well\', u\'GFP\'\x3A u\'Well\'}, {u\'DAPI\'\x3A u\'Site\', u\'TRITC\'\x3A None, u\'TL\'\x3A u\'Site\', u\'GFP\'\x3A u\'Site\'}\x5D
Image set matching method:Metadata
Set intensity range from:Image metadata
Assignments count:4
Single images count:0
Select the rule criteria:and (file does contain "w1")
Name to assign these images:DAPI
Name to assign these objects:Cell
Select the image type:Grayscale image
Set intensity range from:Image bit-depth
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "w5")
Name to assign these images:TL
Name to assign these objects:Nucleus
Select the image type:Grayscale image
Set intensity range from:Image bit-depth
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "w2")
Name to assign these images:GFP
Name to assign these objects:Cytoplasm
Select the image type:Grayscale image
Set intensity range from:Image bit-depth
Retain outlines of loaded objects?:No
Name the outline image:LoadedOutlines
Select the rule criteria:and (file does contain "w4")
Name to assign these images:TRITC
Name to assign these objects:Speckle
Select the image type:Grayscale 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.\', \'---\', \'Settings converted from legacy pipeline.\'\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
IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:10|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 primary objects to be identified:Nuclei
Typical diameter of objects, in pixel units (Min,Max):15,90
Discard objects outside the diameter range?:Yes
Try to merge too small objects with nearby larger objects?:Yes
Discard objects touching the border of the image?:Yes
Method to distinguish clumped objects:Shape
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
Speed up by using lower-resolution image to find local maxima?:No
Name the outline image:PrimaryOutlines
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
Retain outlines of the identified objects?:No
Automatically calculate the threshold using the Otsu method?:Yes
Enter Laplacian of Gaussian threshold:0.5
Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes
Enter LoG filter diameter:5
Handling of objects if excessive number of objects identified:Continue
Maximum number of objects:500
Threshold setting version:1
Threshold strategy:Global
Thresholding method:Otsu
Select the smoothing method for thresholding:Automatic
Threshold smoothing scale:1
Threshold correction factor:1.1
Lower and upper bounds on threshold:0,1.0
Approximate fraction of image covered by objects?:0.9
Manual threshold:0.0
Select the measurement to threshold with:None
Select binary image:None
Masking objects:From image
Two-class or three-class thresholding?:Two classes
Minimize the weighted variance or the entropy?:Weighted variance
Assign pixels in the middle intensity class to the foreground or the background?:Foreground
Method to calculate adaptive window size:Image size
Size of adaptive window:10
IdentifySecondaryObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:9|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input objects:Nuclei
Name the objects to be identified:Cells
Select the method to identify the secondary objects:Watershed - Image
Select the input image:TL
Number of pixels by which to expand the primary objects:10
Regularization factor:0.05
Name the outline image:SecondaryOutlines
Retain outlines of the identified secondary objects?:No
Discard secondary objects touching the border of the image?:No
Discard the associated primary objects?:No
Name the new primary objects:FilteredNuclei
Retain outlines of the new primary objects?:No
Name the new primary object outlines:FilteredNucleiOutlines
Fill holes in identified objects?:Yes
Threshold setting version:1
Threshold strategy:Automatic
Thresholding method:Otsu
Select the smoothing method for thresholding:No smoothing
Threshold smoothing scale:1.0
Threshold correction factor:1.0
Lower and upper bounds on threshold:0.0,1.0
Approximate fraction of image covered by objects?:0.01
Manual threshold:0.0
Select the measurement to threshold with:None
Select binary image:None
Masking objects:None
Two-class or three-class thresholding?:Two classes
Minimize the weighted variance or the entropy?:Weighted variance
Assign pixels in the middle intensity class to the foreground or the background?:Foreground
Method to calculate adaptive window size:Image size
Size of adaptive window:10
MeasureObjectIntensity:[module_num:7|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]
Hidden:3
Select an image to measure:DAPI
Select an image to measure:GFP
Select an image to measure:TRITC
Select objects to measure:Cells
ExportToSpreadsheet:[module_num:8|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?:Yes
Limit output to a size that is allowed in Excel?:No
Select the measurements to export:No
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\x7CNone
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?:Yes
Press button to select measurements to export:
Representation of Nan/Inf:NaN
Add a prefix to file names?:No
Filename prefix\x3A:MyExpt_
Overwrite without warning?:Yes
Data to export:Do not use
Combine these object measurements with those of the previous object?:No
File name:DATA.csv
Use the object name for the file name?:Yes