CellProfiler Pipeline: http://www.cellprofiler.org Version:3 DateRevision:20150922153850 GitHash:Unknown rev. ModuleCount:5 HasImagePlaneDetails:False LoadImages:[module_num:1|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] File type to be loaded:individual images File selection method:Text-Regular expressions Number of images in each group?:3 Type the text that the excluded images have in common:Do not use Analyze all subfolders within the selected folder?:None Input image file location:Default Input Folder\x7C 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:2 Text that these images have in common (case-sensitive):DAPI Position of this image in each group:1 Extract metadata from where?:None Regular expression that finds metadata in the file name:^(?P.*)_(?P\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P\x5B0-9\x5D) Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\\\\\/\x5D(?P.*)\x5B\\\\\\\\/\x5D(?P.*)$ 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:DNA Name this loaded object:Nuclei Retain outlines of loaded objects?:No Name the outline image:LoadedImageOutlines Channel number:1 Rescale intensities?:Yes Text that these images have in common (case-sensitive):GFP Position of this image in each group:2 Extract metadata from where?:None Regular expression that finds metadata in the file name:^(?P.*)_(?P\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P\x5B0-9\x5D) Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\\\\\/\x5D(?P.*)\x5B\\\\\\\\/\x5D(?P.*)$ 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:Pathogen Name this loaded object:Nuclei Retain outlines of loaded objects?:No Name the outline image:LoadedImageOutlines Channel number:1 Rescale intensities?:Yes CorrectIlluminationCalculate:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the input image:DNA Name the output image:IllumDNA Select how the illumination function is calculated:Regular Dilate objects in the final averaged image?:No Dilation radius:1 Block size:60 Rescale the illumination function?:Yes Calculate function for each image individually, or based on all images?:All\x3A Across cycles Smoothing method:Median Filter Method to calculate smoothing filter size:Manually Approximate object size:10 Smoothing filter size:512 Retain the averaged image?:No Name the averaged image:IllumBlueAvg Retain the dilated image?:No Name the dilated image:IllumBlueDilated Automatically calculate spline parameters?:Yes Background mode:auto Number of spline points:5 Background threshold:2.0 Image resampling factor:2.0 Maximum number of iterations:40 Residual value for convergence:0.001 CorrectIlluminationCalculate:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the input image:Pathogen Name the output image:IllumPathogen Select how the illumination function is calculated:Regular Dilate objects in the final averaged image?:No Dilation radius:1 Block size:60 Rescale the illumination function?:Yes Calculate function for each image individually, or based on all images?:All\x3A Across cycles Smoothing method:Median Filter Method to calculate smoothing filter size:Manually Approximate object size:10 Smoothing filter size:512 Retain the averaged image?:No Name the averaged image:IllumBlueAvg Retain the dilated image?:No Name the dilated image:IllumBlueDilated Automatically calculate spline parameters?:Yes Background mode:auto Number of spline points:5 Background threshold:2.0 Image resampling factor:2.0 Maximum number of iterations:40 Residual value for convergence:0.001 SaveImages:[module_num:4|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 type of image to save:Image Select the image to save:IllumDNA Select the objects to save:None Select the module display window to save:None Select method for constructing file names:Single name Select image name for file prefix:None Enter single file name:IllumDNA Number of digits:4 Append a suffix to the image file name?:No Text to append to the image name: Saved file format:mat Output file location:Default Output Folder\x7C Image bit depth:16 Overwrite existing files without warning?:Yes When to save:Last cycle Rescale the images? :No Save as grayscale or color image?:Grayscale Select colormap:gray Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...\x7C Saved movie format:avi SaveImages:[module_num:5|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 type of image to save:Image Select the image to save:IllumPathogen Select the objects to save:None Select the module display window to save:None Select method for constructing file names:Single name Select image name for file prefix:None Enter single file name:IllumPathogen Number of digits:4 Append a suffix to the image file name?:No Text to append to the image name: Saved file format:mat Output file location:Default Output Folder\x7C Image bit depth:16 Overwrite existing files without warning?:Yes When to save:Last cycle Rescale the images? :No Save as grayscale or color image?:Grayscale Select colormap:gray Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...\x7C Saved movie format:avi