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parameter_text_for_Cell_profiler_script_pH_fiber.txt
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parameter_text_for_Cell_profiler_script_pH_fiber.txt
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CellProfiler Pipeline: http://www.cellprofiler.org
Version: 4
DateRevision: 318
GitHash:
ModuleCount: 11
HasImagePlaneDetails: False
Images:
Filter images?: Images only
Select the rule criteria: Find (extension does image) (directory does not contain regex "[\\\\/]")
Metadata:
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})(?P<Site>[0-9])(?P<ChannelNumber>[0-9])$
Regular expression to extract from folder name: (?P<Date>[0-9]{4})(?P<Month>[0-9]{2})(?P<Day>[0-9]{2})$
Extract metadata from: All images
Select the filtering criteria: Find (file does contain "")
Metadata file location: Elsewhere...
Match file and image metadata: []
Use case insensitive matching?: No
Metadata file name: None
NamesAndTypes:
Assign a name to: All images
Select the image type: Grayscale image
Name to assign these images: DNA
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: Find (file does contain "")
Name to assign these objects: Cell
Maximum intensity: 255.0
Groups:
Do you want to group your images?: No
Grouping metadata count: 1
Metadata category: None
IdentifyPrimaryObjects:
Select the input image: DNA
Name the primary objects to be identified: Rectangles
Typical diameter of objects, in pixel units (Min,Max): 2, 600
Discard objects outside the diameter range?: Yes
Discard objects touching the border of the image?: Yes
Method to distinguish clumped objects: None
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: 7.0
Speed up by using lower-resolution image to find local maxima?: Yes
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
Handling of objects if excessive number of objects identified: Continue
Maximum number of objects: 500
Use advanced settings?: Yes
Threshold setting version: 10
Threshold strategy: Adaptive
Thresholding method: RobustBackground
Threshold smoothing scale: 1.3
Threshold correction factor: 1.0
Lower and upper bounds on threshold: 0.007, 1.0
Manual threshold: 0.0
Two-class or three-class thresholding?: Two classes
Assign pixels in the middle intensity class to the foreground or the background?: Foreground
Size of adaptive window: 180
Lower outlier fraction: 0.005
Upper outlier fraction: 0.0
Averaging method: Mean
Variance method: Standard deviation
# of deviations: 2.0
Thresholding method: Otsu
OverlayOutlines:
Display outlines on a blank image?: No
Select image on which to display outlines: DNA
Name the output image: Overlay
Outline display mode: Color
Select method to determine brightness of outlines: Max of image
How to outline: Inner
Select outline color: Red
Select objects to display: Rectangles
SaveImages:
Select the type of image to save: Movie
Select the image to save: Overlay
Select method for constructing file names: From image filename
Select image name for file prefix: DNA
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: _overlay
Saved file format: tiff
Output file location: Same folder as image|
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...
Tile:
Select an input image: DNA
Name the output image: TiledImage
Tile assembly method: Within cycles
Final number of rows: 1
Final number of columns: 3
Image corner to begin tiling: top left
Direction to begin tiling: row
Use meander mode?: No
Automatically calculate number of rows?: No
Automatically calculate number of columns?: No
Select an additional image to tile: DNA
Select an additional image to tile: Overlay
SaveImages:
Select the type of image to save: Movie
Select the image to save: TiledImage
Select method for constructing file names: From image filename
Select image name for file prefix: DNA
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: _tile
Saved file format: tiff
Output file location: Same folder as image|
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...
MeasureObjectSizeShape:
Select objects to measure: Rectangles
Calculate the Zernike features?: No
ExportToSpreadsheet:
Select the column delimiter: Comma (",")
Add image metadata columns to your object data file?: No
Select the measurements to export: None
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: Elsewhere...|/Volumes/Scope Data/Hao_pHFiber_001_pH018015minutespH035and037_001
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