CellProfiler Pipeline: http://www.cellprofiler.org Version:3 DateRevision:20160418141927 GitHash:9969f42 ModuleCount:11 HasImagePlaneDetails:False Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'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.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] : Filter images?:Images only Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\x5B\\\\\\\\\\\\\\\\/\x5D\\\\\\\\.") Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'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.\'\x5D|batch_state:array(\x5B\x5D, 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:^(?P.*)_(?P\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P\x5B0-9\x5D)_w(?P\x5B0-9\x5D) Regular expression:(?P\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$ Extract metadata from:All images Select the filtering criteria:and (file does contain "") Metadata file location: Match file and image metadata:\x5B\x5D Use case insensitive matching?:No NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Assign a name to:All images Select the image type:Grayscale image Name to assign these images:GFP Match metadata:\x5B\x5D Image set matching method:Order Set intensity range from:Image metadata Assignments count:1 Single images count:0 Maximum intensity:255.0 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 Retain outlines of loaded objects?:No Name the outline image:LoadedOutlines Maximum intensity:255.0 Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'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.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Do you want to group your images?:No grouping metadata count:1 Metadata category:None EnhanceOrSuppressFeatures:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the input image:GFP Name the output image:FilteredGFP Select the operation:Enhance Feature size:30 Feature type:Speckles Range of hole sizes:1,10 Smoothing scale:2.0 Shear angle:0.0 Decay:0.95 Enhancement method:Tubeness Speed and accuracy:Fast / hexagonal IdentifyPrimaryObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:10|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the input image:FilteredGFP Name the primary objects to be identified:Area Typical diameter of objects, in pixel units (Min,Max):1,10000 Discard objects outside the diameter range?:No Try to merge too small objects with nearby larger objects?:No Discard objects touching the border of the image?:No 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 Name the outline image:AreaOccupied Fill holes in identified objects?:Never Automatically calculate size of smoothing filter for declumping?:Yes Automatically calculate minimum allowed distance between local maxima?:Yes Retain outlines of the identified objects?:Yes Automatically calculate the threshold using the Otsu method?:Yes Enter Laplacian of Gaussian threshold:0.5 Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes Enter LoG filter diameter:5.0 Handling of objects if excessive number of objects identified:Continue Maximum number of objects:500 Threshold setting version:2 Threshold strategy:Manual Thresholding method:Otsu Select the smoothing method for thresholding:Automatic Threshold smoothing scale:1.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.0,1.0 Approximate fraction of image covered by objects?:0.01 Manual threshold:0.0000001 Select the measurement to threshold with:None Select binary image:None Masking objects:None 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 Method to calculate adaptive window size:Image size Size of adaptive window:10 Use default parameters?:Default Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 MeasureImageIntensity:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the image to measure:GFP Measure the intensity only from areas enclosed by objects?:Yes Select the input objects:Area IdentifyPrimaryObjects:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:10|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the input image:FilteredGFP Name the primary objects to be identified:GFPpositive Typical diameter of objects, in pixel units (Min,Max):9,100 Discard objects outside the diameter range?:Yes Try to merge too small objects with nearby larger objects?:No Discard objects touching the border of the image?:No Method to distinguish clumped objects:Shape Method to draw dividing lines between clumped objects:Propagate Size of smoothing filter:10 Suppress local maxima that are closer than this minimum allowed distance:10 Speed up by using lower-resolution image to find local maxima?:No Name the outline image:PrimaryOutlines Fill holes in identified objects?:Never Automatically calculate size of smoothing filter for declumping?:Yes Automatically calculate minimum allowed distance between local maxima?:No Retain outlines of the identified objects?:No Automatically calculate the threshold using the Otsu method?:Yes Enter Laplacian of Gaussian threshold:0.5 Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes Enter LoG filter diameter:5.0 Handling of objects if excessive number of objects identified:Continue Maximum number of objects:500 Threshold setting version:2 Threshold strategy:Measurement Thresholding method:Otsu Select the smoothing method for thresholding:Automatic Threshold smoothing scale:1.0 Threshold correction factor:1.5 Lower and upper bounds on threshold:0.15,0.35 Approximate fraction of image covered by objects?:0.01 Manual threshold:0.23 Select the measurement to threshold with:Intensity_MedianIntensity_GFP_Area Select binary image:None Masking objects:None 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 Method to calculate adaptive window size:Image size Size of adaptive window:10 Use default parameters?:Default Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 MeasureObjectSizeShape:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select objects to measure:GFPpositive Select objects to measure:Area Calculate the Zernike features?:Yes FilterObjects:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Name the output objects:FilteredGFPpositive Select the object to filter:GFPpositive Select the filtering mode:Measurements Select the filtering method:Limits Select the objects that contain the filtered objects:None Retain outlines of the identified objects?:No Name the outline image:FilteredObjects Rules file location:Elsewhere...\x7C Rules file name:rules.txt Class number:1 Measurement count:1 Additional object count:0 Assign overlapping child to:Both parents Select the measurement to filter by:AreaShape_Eccentricity Filter using a minimum measurement value?:No Minimum value:0.5 Filter using a maximum measurement value?:Yes Maximum value:0.94 ExportToSpreadsheet:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the column delimiter:Comma (",") Add image metadata columns to your object data file?:No Limit output to a size that is allowed in Excel?:No Select the measurements to export:No Calculate the per-image mean values for object measurements?:Yes Calculate the per-image median values for object measurements?:No Calculate the per-image standard deviation values for object measurements?:Yes Output file location:Default Input Folder sub-folder\x7CDesktop 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 :FilteredGFPpositive\x7CLocation_Center_Y,FilteredGFPpositive\x7CLocation_Center_X,FilteredGFPpositive\x7CNumber_Object_Number,FilteredGFPpositive\x7CParent_GFPpositive,Image\x7CCount_FilteredGFPpositive,Image\x7CCount_GFPpositive,Image\x7CGroup_Index,Image\x7CGroup_Number,Image\x7CWidth_GFP,Image\x7CExecutionTime_01Images,Image\x7CExecutionTime_04Groups,Image\x7CExecutionTime_02Metadata,Image\x7CExecutionTime_03NamesAndTypes,Image\x7CExecutionTime_06IdentifyPrimaryObjects,Image\x7CExecutionTime_09SaveImages,Image\x7CExecutionTime_07MeasureObjectSizeShape,Image\x7CExecutionTime_08FilterObjects,Image\x7CExecutionTime_05EnhanceOrSuppressFeatures,Image\x7CSeries_GFP,Image\x7CFrame_GFP,Image\x7CURL_GFP,Image\x7CMD5Digest_GFP,Image\x7CFileName_GFP,Image\x7CScaling_GFP,Image\x7CModuleError_01Images,Image\x7CModuleError_04Groups,Image\x7CModuleError_02Metadata,Image\x7CModuleError_03NamesAndTypes,Image\x7CModuleError_06IdentifyPrimaryObjects,Image\x7CModuleError_09SaveImages,Image\x7CModuleError_07MeasureObjectSizeShape,Image\x7CModuleError_08FilterObjects,Image\x7CModuleError_05EnhanceOrSuppressFeatures,Image\x7CPathName_GFP,Image\x7CThreshold_OrigThreshold_GFPpositive,Image\x7CThreshold_SumOfEntropies_GFPpositive,Image\x7CThreshold_WeightedVariance_GFPpositive,Image\x7CThreshold_FinalThreshold_GFPpositive,Image\x7CHeight_GFP,GFPpositive\x7CLocation_Center_Y,GFPpositive\x7CLocation_Center_X,GFPpositive\x7CAreaShape_Perimeter,GFPpositive\x7CAreaShape_FormFactor,GFPpositive\x7CAreaShape_MeanRadius,GFPpositive\x7CAreaShape_Center_Y,GFPpositive\x7CAreaShape_Center_X,GFPpositive\x7CAreaShape_MajorAxisLength,GFPpositive\x7CAreaShape_MinFeretDiameter,GFPpositive\x7CAreaShape_EulerNumber,GFPpositive\x7CAreaShape_Area,GFPpositive\x7CAreaShape_MaxFeretDiameter,GFPpositive\x7CAreaShape_Solidity,GFPpositive\x7CAreaShape_Zernike_1_1,GFPpositive\x7CAreaShape_Zernike_0_0,GFPpositive\x7CAreaShape_Zernike_3_1,GFPpositive\x7CAreaShape_Zernike_3_3,GFPpositive\x7CAreaShape_Zernike_2_0,GFPpositive\x7CAreaShape_Zernike_2_2,GFPpositive\x7CAreaShape_Zernike_5_1,GFPpositive\x7CAreaShape_Zernike_5_3,GFPpositive\x7CAreaShape_Zernike_5_5,GFPpositive\x7CAreaShape_Zernike_4_0,GFPpositive\x7CAreaShape_Zernike_4_2,GFPpositive\x7CAreaShape_Zernike_4_4,GFPpositive\x7CAreaShape_Zernike_7_1,GFPpositive\x7CAreaShape_Zernike_7_3,GFPpositive\x7CAreaShape_Zernike_7_5,GFPpositive\x7CAreaShape_Zernike_7_7,GFPpositive\x7CAreaShape_Zernike_6_2,GFPpositive\x7CAreaShape_Zernike_6_0,GFPpositive\x7CAreaShape_Zernike_6_6,GFPpositive\x7CAreaShape_Zernike_6_4,GFPpositive\x7CAreaShape_Zernike_9_1,GFPpositive\x7CAreaShape_Zernike_9_3,GFPpositive\x7CAreaShape_Zernike_9_5,GFPpositive\x7CAreaShape_Zernike_9_7,GFPpositive\x7CAreaShape_Zernike_9_9,GFPpositive\x7CAreaShape_Zernike_8_0,GFPpositive\x7CAreaShape_Zernike_8_2,GFPpositive\x7CAreaShape_Zernike_8_4,GFPpositive\x7CAreaShape_Zernike_8_6,GFPpositive\x7CAreaShape_Zernike_8_8,GFPpositive\x7CAreaShape_MedianRadius,GFPpositive\x7CAreaShape_Compactness,GFPpositive\x7CAreaShape_Extent,GFPpositive\x7CAreaShape_Eccentricity,GFPpositive\x7CAreaShape_MaximumRadius,GFPpositive\x7CAreaShape_MinorAxisLength,GFPpositive\x7CAreaShape_Orientation,GFPpositive\x7CNumber_Object_Number,GFPpositive\x7CChildren_FilteredGFPpositive_Count Representation of Nan/Inf:NaN Add a prefix to file names?:Yes Filename prefix:test_ Overwrite existing files without warning?:No Data to export:Image Combine these object measurements with those of the previous object?:No File name:DATA.csv Use the object name for the file name?:Yes Data to export:FilteredGFPpositive Combine these object measurements with those of the previous object?:No File name:DATA.csv Use the object name for the file name?:Yes