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added segmentation pipeline for CellProfiler
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| CellProfiler Pipeline: http://www.cellprofiler.org | ||
| Version:3 | ||
| DateRevision:20160418141927 | ||
| GitHash:9969f42 | ||
| ModuleCount:4 | ||
| HasImagePlaneDetails:False | ||
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| LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] | ||
| Input data file location:Default Input Folder\x7C | ||
| Name of the file:input_file.csv | ||
| Load images based on this data?:Yes | ||
| Base image location:Default Input Folder\x7C/jr0th/data/BBBC022/raw/unzipped/ | ||
| Process just a range of rows?:No | ||
| Rows to process:1,100000 | ||
| Group images by metadata?:No | ||
| Select metadata tags for grouping: | ||
| Rescale intensities?:No | ||
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| IdentifyPrimaryObjects:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:10|show_window:False|notes:\x5B\x5D|batch_state:array(\'\', \n dtype=\'\x7CS1\')|enabled:True|wants_pause:False] | ||
| Select the input image:DNA | ||
| Name the primary objects to be identified:Nuclei | ||
| Typical diameter of objects, in pixel units (Min,Max):15,150 | ||
| 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:Shape | ||
| Size of smoothing filter:20 | ||
| Suppress local maxima that are closer than this minimum allowed distance:20 | ||
| Speed up by using lower-resolution image to find local maxima?:Yes | ||
| Name the outline image:NucleiOutlines | ||
| Fill holes in identified objects?:After both thresholding and declumping | ||
| Automatically calculate size of smoothing filter for declumping?:No | ||
| 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 | ||
| Handling of objects if excessive number of objects identified:Continue | ||
| Maximum number of objects:500 | ||
| Threshold setting version:1 | ||
| Threshold strategy:Global | ||
| Thresholding method:Otsu | ||
| Select the smoothing method for thresholding:Automatic | ||
| Threshold smoothing scale:1 | ||
| Threshold correction factor:1 | ||
| Lower and upper bounds on threshold:0.003,1.0 | ||
| Approximate fraction of image covered by objects?:0.01 | ||
| Manual threshold:0.0 | ||
| Select the measurement to threshold with:None | ||
| Select binary image:None | ||
| Masking objects:From image | ||
| 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 | ||
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| ConvertObjectsToImage:[module_num:3|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 the input objects:Nuclei | ||
| Name the output image:NucleiMask | ||
| Select the color format:Grayscale | ||
| Select the colormap:Default | ||
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| 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:NucleiMask | ||
| Select the objects to save:None | ||
| Select the module display window to save:None | ||
| 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?:No | ||
| Text to append to the image name:_mask | ||
| Saved file format:tiff | ||
| Output file location:Default Output Folder sub-folder\x7Cmask | ||
| Image bit depth:16-bit integer | ||
| Overwrite existing files without warning?:Yes | ||
| When to save:Every 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 |