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Export Intensity Data - Marker vs. Target.cp
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Export Intensity Data - Marker vs. Target.cp
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CellProfiler Pipeline: http://www.cellprofiler.org
Version:2
DateRevision:20130109170729
LoadImages:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5Bu\'Load each channel of the image to be analyzed this round.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)]
File type to be loaded:individual images
File selection method:Text-Exact match
Number of images in each group?:3
Type the text that the excluded images have in common:Median
Analyze all subfolders within the selected folder?:All
Input image file location:Default Input Folder sub-folder\x7CCorrected Images
Check image sets for unmatched or duplicate files?:Yes
Group images by metadata?:No
Exclude certain files?:No
Specify metadata fields to group by:
Select subfolders to analyze:
Image count:3
Text that these images have in common (case-sensitive):Ch3-T1
Position of this image in each group:1
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:\\\\((?P<Strain>.*) (?P<Colony>\\\\S*) (?P<Field>\\\\S*)\\\\)
Type the regular expression that finds metadata in the subfolder path:.*\\\\\\\\(?P<Strain>.*) (?P<Condition>.*) (?P<Field>.*).lsm
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:3
Load the input as images or objects?:Images
Name this loaded image:NLStdTom
Name this loaded object:Nuclei
Retain outlines of loaded objects?:No
Name the outline image:LoadedImageOutlines
Channel number:1
Rescale intensities?:No
Text that these images have in common (case-sensitive):Ch2-T3
Position of this image in each group:2
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:\\\\((?P<Strain>.*) (?P<Colony>\\\\S*) (?P<Field>\\\\S*)\\\\)
Type the regular expression that finds metadata in the subfolder path:.*\\\\\\\\(?P<Strain>.*) (?P<Condition>.*) (?P<Field>.*).lsm
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:3
Load the input as images or objects?:Images
Name this loaded image:MTSmCer
Name this loaded object:Nuclei
Retain outlines of loaded objects?:No
Name the outline image:LoadedImageOutlines
Channel number:1
Rescale intensities?:No
Text that these images have in common (case-sensitive):Ch2-T2
Position of this image in each group:3
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:\\\\((?P<Strain>.*) (?P<Colony>\\\\S*) (?P<Field>\\\\S*)\\\\)
Type the regular expression that finds metadata in the subfolder path:.*\\\\\\\\(?P<Strain>.*) (?P<Condition>.*) (?P<Field>.*).lsm
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:3
Load the input as images or objects?:Images
Name this loaded image:GFP
Name this loaded object:Nuclei
Retain outlines of loaded objects?:No
Name the outline image:LoadedImageOutlines
Channel number:1
Rescale intensities?:No
LoadImages:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\'Load cell, nuclei, mitochondria, and cytosol objects.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)]
File type to be loaded:individual images
File selection method:Text-Exact match
Number of images in each group?:3
Type the text that the excluded images have in common:Median
Analyze all subfolders within the selected folder?:All
Input image file location:Default Input Folder sub-folder\x7CObjects
Check image sets for unmatched or duplicate files?:Yes
Group images by metadata?:No
Exclude certain files?:No
Specify metadata fields to group by:
Select subfolders to analyze:
Image count:4
Text that these images have in common (case-sensitive):Cells Filtered (
Position of this image in each group:1
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:\\\\((?P<Strain>.*) (?P<Colony>\\\\S*) (?P<Field>\\\\S*)\\\\)
Type the regular expression that finds metadata in the subfolder path:.*\\\\\\\\(?P<Strain>.*) - Colony (?P<Colony>.*) - Field (?P<Field>.*).lsm
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:3
Load the input as images or objects?:Objects
Name this loaded image:CellsImage
Name this loaded object:Cells
Retain outlines of loaded objects?:No
Name the outline image:LoadedImageOutlines
Channel number:1
Rescale intensities?:No
Text that these images have in common (case-sensitive):Pure Nuclei (
Position of this image in each group:2
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:\\\\((?P<Strain>.*) (?P<Colony>\\\\S*) (?P<Field>\\\\S*)\\\\)
Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\\\\\/\x5D(?P<Date>.*)\x5B\\\\\\\\/\x5D(?P<Run>.*)$
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:3
Load the input as images or objects?:Objects
Name this loaded image:NucleiImage
Name this loaded object:Nuclei
Retain outlines of loaded objects?:No
Name the outline image:LoadedImageOutlines
Channel number:1
Rescale intensities?:No
Text that these images have in common (case-sensitive):Pure Mitochondria (
Position of this image in each group:3
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:\\\\((?P<Strain>.*) (?P<Colony>\\\\S*) (?P<Field>\\\\S*)\\\\)
Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\\\\\/\x5D(?P<Date>.*)\x5B\\\\\\\\/\x5D(?P<Run>.*)$
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:3
Load the input as images or objects?:Objects
Name this loaded image:MitochondriaImage
Name this loaded object:Mitochondria
Retain outlines of loaded objects?:No
Name the outline image:LoadedImageOutlines
Channel number:1
Rescale intensities?:No
Text that these images have in common (case-sensitive):Cytosol (
Position of this image in each group:4
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:\\\\((?P<Strain>.*) (?P<Colony>\\\\S*) (?P<Field>\\\\S*)\\\\)
Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\\\\\/\x5D(?P<Date>.*)\x5B\\\\\\\\/\x5D(?P<Run>.*)$
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:3
Load the input as images or objects?:Objects
Name this loaded image:CytosolImage
Name this loaded object:Cytosol
Retain outlines of loaded objects?:No
Name the outline image:LoadedImageOutlines
Channel number:1
Rescale intensities?:No
Smooth:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\'Smooth the image subtly to remove the influence of noise.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)]
Select the input image:NLStdTom
Name the output image:NLStdTomFiltered
Select smoothing method:Median Filter
Calculate artifact diameter automatically?:No
Typical artifact diameter, in pixels:2
Edge intensity difference:0.1
Smooth:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\'Smooth the image subtly to remove the influence of noise.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)]
Select the input image:MTSmCer
Name the output image:MTSmCerFiltered
Select smoothing method:Median Filter
Calculate artifact diameter automatically?:No
Typical artifact diameter, in pixels:2
Edge intensity difference:0.1
Smooth:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\'Smooth the image subtly to remove the influence of noise.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)]
Select the input image:GFP
Name the output image:GFPFiltered
Select smoothing method:Median Filter
Calculate artifact diameter automatically?:No
Typical artifact diameter, in pixels:2
Edge intensity difference:0.1
ImageMath:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Apply crosstalk correction for NLStdTom and MTSmCer signal appearing in GFP channel.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)]
Operation:Add
Raise the power of the result by:1
Multiply the result by:1
Add to result:0
Set values less than 0 equal to 0?:Yes
Set values greater than 1 equal to 1?:Yes
Ignore the image masks?:No
Name the output image:GFPFilteredCrosstalkCorrected
Image or measurement?:Image
Select the first image:GFPFiltered
Multiply the first image by:1
Measurement:
Image or measurement?:Image
Select the second image:NLStdTomFiltered
Multiply the second image by:-0.0145417
Measurement:
Image or measurement?:Image
Select the third image:MTSmCerFiltered
Multiply the third image by:-0.0838191
Measurement:
MeasureObjectIntensity:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)]
Hidden:3
Select an image to measure:GFPFilteredCrosstalkCorrected
Select an image to measure:NLStdTomFiltered
Select an image to measure:MTSmCerFiltered
Select objects to measure:Cells
Select objects to measure:Nuclei
Select objects to measure:Mitochondria
Select objects to measure:Cytosol
ExportToSpreadsheet:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\'Save the data.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)]
Select or enter the column delimiter:Comma (",")
Prepend the output file name to the data file names?:Yes
Add image metadata columns to your object data file?:Yes
Limit output to a size that is allowed in Excel?:No
Select the columns of 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 sub-folder\x7COutput Data
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 measurements, using default file names?:No
Press button to select measurements to export:Mitochondria\x7CIntensity_MeanIntensity_MTSmCerFiltered,Mitochondria\x7CIntensity_MeanIntensity_GFPFilteredCrosstalkCorrected,Nuclei\x7CIntensity_MeanIntensity_NLStdTomFiltered,Nuclei\x7CIntensity_MeanIntensity_GFPFilteredCrosstalkCorrected
Data to export:Nuclei
Combine these object measurements with those of the previous object?:No
File name:Marker Target Correlation Data.csv
Use the object name for the file name?:No
Data to export:Mitochondria
Combine these object measurements with those of the previous object?:Yes
File name:Nuclei GFP Intensities.csv
Use the object name for the file name?:No