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test.cppipe
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test.cppipe
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CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:421
GitHash:
ModuleCount:5
HasImagePlaneDetails:False
LoadData:[module_num:1|svn_version:'Unknown'|variable_revision_number:6|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Input data file location:Default Input Folder sub-folder|
Name of the file:images.csv
Load images based on this data?:Yes
Base image location:None|
Process just a range of rows?:No
Rows to process:1,100000
Group images by metadata?:Yes
Select metadata tags for grouping:Plate,WellRow
Rescale intensities?:No
MeasureImageQuality:[module_num:2|svn_version:'Unknown'|variable_revision_number:6|show_window:False|notes:['Generate image quality measurements for all channels. Image features made here include image blur measurements at multiple spatial scales, saturation metrics, and intensity-based measures.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Calculate metrics for which images?:All loaded images
Image count:1
Scale count:4
Threshold count:1
Select the images to measure:
Include the image rescaling value?:Yes
Calculate blur metrics?:Yes
Spatial scale for blur measurements:2
Spatial scale for blur measurements:5
Spatial scale for blur measurements:10
Spatial scale for blur measurements:20
Calculate saturation metrics?:Yes
Calculate intensity metrics?:Yes
Calculate thresholds?:No
Use all thresholding methods?:Yes
Select a thresholding method:Otsu
Typical fraction of the image covered by objects:0.1
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
MeasureImageQuality:[module_num:3|svn_version:'Unknown'|variable_revision_number:6|show_window:False|notes:['In addition to the more general image QC features, collect the thresholds for the DNA and RNA images. We use these two channels because the DNA image is used for nuclei identification and the RNA image is used for cell body identification. Examining the histogram of these values is often helpful in setting the lower threshold bound, as well as getting a sense of what outliers look like.', '', 'Note that different threshold methods are calculated for each channel, although more could be added. Also note that even though the channels will be illumination corrected in the feature extraction pipeline, we have not found that it affects QC assessment substantially.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Calculate metrics for which images?:Select...
Image count:2
Scale count:1
Threshold count:1
Scale count:1
Threshold count:1
Select the images to measure:CY5, OrigDAPI, OrigGFP, TexasRed
Include the image rescaling value?:No
Calculate blur metrics?:No
Spatial scale for blur measurements:20
Calculate saturation metrics?:No
Calculate intensity metrics?:No
Calculate thresholds?:Yes
Use all thresholding methods?:No
Select a thresholding method:Otsu
Typical fraction of the image covered by objects:0.1
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?:Background
Select the images to measure:CY5, OrigDAPI, OrigGFP, TexasRed
Include the image rescaling value?:No
Calculate blur metrics?:No
Spatial scale for blur measurements:20
Calculate saturation metrics?:No
Calculate intensity metrics?:No
Calculate thresholds?:Yes
Use all thresholding methods?:No
Select a thresholding method:Otsu
Typical fraction of the image covered by objects:0.1
Two-class or three-class thresholding?:Three classes
Minimize the weighted variance or the entropy?:Weighted variance
Assign pixels in the middle intensity class to the foreground or the background?:Foreground
ExportToDatabase:[module_num:4|svn_version:'Unknown'|variable_revision_number:28|show_window:False|notes:['Write the quality control measurements to the database of your choice, and create a properties file for exploring the data with CellProfiler Analyst. A CellProfiler Analyst properties file and workspace file are also created as well.', '', 'Change the table prefix to same as the folder (tables cannot start with a number)']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Database type:SQLite
Database name:hummingbird
Add a prefix to table names?:Yes
Table prefix:qc_offset
Output file location:Elsewhere...|Y:\\Microglia_Morphology_Project\\Kanupriya\\MSCEV Frozen Studies
Create a CellProfiler Analyst properties file?:Yes
Database host:hummingbird.cgt7x2kyja4j.us-east-2.rds.amazonaws.com
Username:admin
Password:hummingbird4CP
Name the SQLite database file:DefaultDB.db
Calculate the per-image mean values of object measurements?:No
Calculate the per-image median values of object measurements?:No
Calculate the per-image standard deviation values of object measurements?:No
Calculate the per-well mean values of object measurements?:No
Calculate the per-well median values of object measurements?:No
Calculate the per-well standard deviation values of object measurements?:No
Export measurements for all objects to the database?:None
Select the objects:
Maximum # of characters in a column name:64
Create one table per object, a single object table or a single object view?:Single object table
Enter an image url prepend if you plan to access your files via http:http://imageweb/images/CPALinks
Write image thumbnails directly to the database?:Yes
Select the images for which you want to save thumbnails:CY5,OrigDAPI,OrigGFP,TexasRed
Auto-scale thumbnail pixel intensities?:Yes
Select the plate type:96
Select the plate metadata:Plate
Select the well metadata:Well
Include information for all images, using default values?:No
Properties image group count:4
Properties group field count:1
Properties filter field count:0
Workspace measurement count:10
Experiment name:FrozenMSCEV_Inhibitor
Which objects should be used for locations?:None
Enter a phenotype class table name if using the Classifier tool in CellProfiler Analyst:
Export object relationships?:No
Overwrite without warning?:Data only
Access CellProfiler Analyst images via URL?:Yes
Select the classification type:Object
Select an image to include:TexasRed
Use the image name for the display?:No
Image name:TR
Channel color:red
Select an image to include:CY5
Use the image name for the display?:No
Image name:CY5
Channel color:magenta
Select an image to include:OrigGFP
Use the image name for the display?:No
Image name:GFP
Channel color:green
Select an image to include:OrigDAPI
Use the image name for the display?:No
Image name:DAPI
Channel color:blue
Do you want to add group fields?:No
Enter the name of the group:
Enter the per-image columns which define the group, separated by commas:ImageNumber, Image_Metadata_Plate, Image_Metadata_Well
Do you want to add filter fields?:No
Automatically create a filter for each plate?:No
Create a CellProfiler Analyst workspace file?:Yes
Select the measurement display tool:ScatterPlot
Type of measurement to plot on the X-axis:Index
Enter the object name:Image
Select the X-axis measurement:
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:Image
Select the Y-axis measurement:ImageQuality_PowerLogLogSlope_TexasRed
Select the Y-axis index:ImageNumber
Select the measurement display tool:ScatterPlot
Type of measurement to plot on the X-axis:Index
Enter the object name:None
Select the X-axis measurement:None
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:None
Select the Y-axis measurement:ImageQuality_PowerLogLogSlope_CY5
Select the Y-axis index:ImageNumber
Select the measurement display tool:ScatterPlot
Type of measurement to plot on the X-axis:Index
Enter the object name:None
Select the X-axis measurement:None
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:None
Select the Y-axis measurement:ImageQuality_PowerLogLogSlope_OrigGFP
Select the Y-axis index:ImageNumber
Select the measurement display tool:ScatterPlot
Type of measurement to plot on the X-axis:Index
Enter the object name:None
Select the X-axis measurement:None
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:None
Select the Y-axis measurement:ImageQuality_PowerLogLogSlope_OrigDAPI
Select the Y-axis index:ImageNumber
Select the measurement display tool:ScatterPlot
Type of measurement to plot on the X-axis:Image
Enter the object name:None
Select the X-axis measurement:ImageQuality_StdIntensity_TexasRed
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:None
Select the Y-axis measurement:ImageQuality_PercentMaximal_TexasRed
Select the Y-axis index:ImageNumber
Select the measurement display tool:ScatterPlot
Type of measurement to plot on the X-axis:Image
Enter the object name:None
Select the X-axis measurement:ImageQuality_StdIntensity_CY5
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:None
Select the Y-axis measurement:ImageQuality_PercentMaximal_CY5
Select the Y-axis index:ImageNumber
Select the measurement display tool:ScatterPlot
Type of measurement to plot on the X-axis:Image
Enter the object name:None
Select the X-axis measurement:ImageQuality_StdIntensity_OrigGFP
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:None
Select the Y-axis measurement:ImageQuality_PercentMaximal_OrigGFP
Select the Y-axis index:ImageNumber
Select the measurement display tool:ScatterPlot
Type of measurement to plot on the X-axis:Image
Enter the object name:None
Select the X-axis measurement:ImageQuality_StdIntensity_OrigDAPI
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:None
Select the Y-axis measurement:ImageQuality_PercentMaximal_OrigDAPI
Select the Y-axis index:ImageNumber
Select the measurement display tool:Histogram
Type of measurement to plot on the X-axis:Image
Enter the object name:None
Select the X-axis measurement:ImageQuality_ThresholdOtsu_OrigDAPI_2W
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:None
Select the Y-axis measurement:None
Select the Y-axis index:ImageNumber
Select the measurement display tool:Histogram
Type of measurement to plot on the X-axis:Image
Enter the object name:None
Select the X-axis measurement:ImageQuality_ThresholdOtsu_TexasRed_3FW
Select the X-axis index:ImageNumber
Type of measurement to plot on the Y-axis:Image
Enter the object name:None
Select the Y-axis measurement:None
Select the Y-axis index:ImageNumber
CreateBatchFiles:[module_num:5|svn_version:'Unknown'|variable_revision_number:8|show_window:False|notes:['This module is used only if running the pipeline on a computing cluster; it is used to convert all paths to the format as seen by the computing node. If not using a computing cluster (i.e, you are running the pipeline locally), disable this module by clicking on the green checkmark to the left of the module name; the checkmark is grayed out when the module is disabled.']|batch_state:array([], dtype=uint8)|enabled:False|wants_pause:False]
Store batch files in default output folder?:Yes
Output folder path:/imaging/analysis/2011_07_13_TargetAccelerator_CancerProgram_MPG/2013_10_11_SIGMA2_Pilot/Output/QC
Are the cluster computers running Windows?:No
Hidden- in batch mode:No
Hidden- in distributed mode:No
Hidden- default input folder at time of save:/imaging/analysis/2011_07_13_TargetAccelerator_CancerProgram_MPG/2013_10_11_SIGMA2_Pilot
Hidden- revision number:20131013183127
Hidden- from old matlab:No
Local root path:
Cluster root path:
Local root path:
Cluster root path: