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thresholding_dev1.cppipe
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thresholding_dev1.cppipe
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CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:421
GitHash:
ModuleCount:7
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:All images
Select the image type:Grayscale image
Name to assign these images:BG
Match metadata:[]
Image set matching method:Order
Set intensity range from:Image metadata
Assignments count:1
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 contain "")
Name to assign these images:DNA
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:['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
Threshold:[module_num:5|svn_version:'Unknown'|variable_revision_number:12|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:BG
Name the output image:Threshold
Threshold strategy:Global
Thresholding method:Robust Background
Threshold smoothing scale:0.0
Threshold correction factor:1.0
Lower and upper bounds on threshold:0.0,1.0
Manual threshold:0.0
Select the measurement to threshold with:None
Two-class or three-class thresholding?:Two classes
Log transform before thresholding?:No
Assign pixels in the middle intensity class to the foreground or the background?:Foreground
Size of adaptive window:50
Lower outlier fraction:0.05
Upper outlier fraction:0.05
Averaging method:Mean
Variance method:Standard deviation
# of deviations:1
Thresholding method:Otsu
SaveImages:[module_num:6|svn_version:'Unknown'|variable_revision_number:16|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select the type of image to save:Image
Select the image to save:Threshold
Select method for constructing file names:From image filename
Select image name for file prefix:BG
Enter single file name:OrigBlue
Number of digits:4
Append a suffix to the image file name?:Yes
Text to append to the image name:_thd
Saved file format:tiff
Output file location:Default Output Folder|
Image bit depth:8-bit integer
Overwrite existing files without warning?:No
When to save:Every cycle
Record the file and path information to the saved image?:No
Create subfolders in the output folder?:No
Base image folder:Elsewhere...|
How to save the series:T (Time)
Save with lossless compression?:No
ExportToSpreadsheet:[module_num:7|svn_version:'Unknown'|variable_revision_number:13|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:False|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:MyExpt_
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