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calculate_intensity.cppipe
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CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:421
GitHash:
ModuleCount:9
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?: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 to extract from file name:^(?P<Plate>.*)_(?P<Well>[A-P][0-9]{2})_s(?P<Site>[0-9])_w(?P<ChannelNumber>[0-9])
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:[{'mask': '', 'original': ''}]
Image set matching method:Order
Set intensity range from:Image metadata
Assignments count:2
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 containregexp "thd")
Name to assign these images:mask
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 doesnot contain "thd")
Name to assign these images:original
Name to assign these objects:Nucleus
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
ImageMath:[module_num:5|svn_version:'Unknown'|variable_revision_number:5|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Operation:Invert
Raise the power of the result by:1.0
Multiply the result by:1.0
Add to result:0.0
Set values less than 0 equal to 0?:Yes
Set values greater than 1 equal to 1?:Yes
Replace invalid values with 0?:Yes
Ignore the image masks?:No
Name the output image:mask_inverted
Image or measurement?:Image
Select the first image:mask
Multiply the first image by:1.0
Measurement:
Image or measurement?:Image
Select the second image:
Multiply the second image by:1.0
Measurement:
Crop:[module_num:6|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:original
Name the output image:Cropped_signal
Select the cropping shape:Image
Select the cropping method:Coordinates
Apply which cycle's cropping pattern?:Every
Left and right rectangle positions:0,end
Top and bottom rectangle positions:0,end
Coordinates of ellipse center:500,500
Ellipse radius, X direction:400
Ellipse radius, Y direction:200
Remove empty rows and columns?:All
Select the masking image:mask
Select the image with a cropping mask:None
Select the objects:None
Crop:[module_num:7|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:original
Name the output image:Cropped_background
Select the cropping shape:Image
Select the cropping method:Coordinates
Apply which cycle's cropping pattern?:Every
Left and right rectangle positions:0,end
Top and bottom rectangle positions:0,end
Coordinates of ellipse center:500,500
Ellipse radius, X direction:400
Ellipse radius, Y direction:200
Remove empty rows and columns?:All
Select the masking image:mask_inverted
Select the image with a cropping mask:None
Select the objects:None
MeasureImageIntensity:[module_num:8|svn_version:'Unknown'|variable_revision_number:4|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select images to measure:Cropped_background, Cropped_signal
Measure the intensity only from areas enclosed by objects?:No
Select input object sets:
Calculate custom percentiles:No
Specify percentiles to measure:10,90
ExportToSpreadsheet:[module_num:9|svn_version:'Unknown'|variable_revision_number:13|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select the column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Add image file and folder names to your object data file?: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|
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:
Representation of Nan/Inf:NaN
Add a prefix to file names?:Yes
Filename prefix:intensity_
Overwrite existing files without warning?:No
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