Journal: Skeletal Muscle

Article Title: Automated muscle histopathology analysis using CellProfiler

doi: 10.1186/s13395-018-0178-6

Figure Lengend Snippet: CellProfiler (version 2.2.0) interface. a The pipeline panel consists of input modules for data entry (image file or folder name, image type, and grouping of images). The analysis modules is the platform to build up the analysis pipeline from the module ‘ColorToGray’ to ExportToSpreadsheet,’ which can be inserted by clicking the ‘+’ sign below the pipeline panel

Article Snippet: Other requirements: MuscleAnalyzer pipeline requires CellProfiler which is freely available from CellProfiler ( http://cellprofiler.org/ ) developed by the Carpenter Lab at the Broad Institute of Harvard and MIT.

Techniques:

Journal: Skeletal Muscle

Article Title: Automated muscle histopathology analysis using CellProfiler

doi: 10.1186/s13395-018-0178-6

Figure Lengend Snippet: Sample image processing by CellProfiler. a Original RBG image of mdx muscle section stained with laminin α2 (green) and DAPI (blue). b , c Converted grayscale images of each channel after running the “ColorToGray” module. d Inverted green channel image. e Pseudo-colored image to show individual muscle fibers identified by using ‘IdentifyPrimaryObjects’ module. f The identified muscle objects were shrunk by seven pixels in order to determine if they contain central nuclei. g Outlines of identified muscle fibers were overlaid with original green channel image to illustrate the accuracy of muscle fiber identification. h Pseudo-colored image to show individual nuclei identified by using ‘IdentifyPrimaryObjects’ module. i The outlines of identified muscle fibers and nuclei were overlaid with original green channel image to illustrate the accuracy of classification with either normal (blue) or central nucleated muscles (red)

Article Snippet: Other requirements: MuscleAnalyzer pipeline requires CellProfiler which is freely available from CellProfiler ( http://cellprofiler.org/ ) developed by the Carpenter Lab at the Broad Institute of Harvard and MIT.

Techniques: Staining, Muscles

Journal: Skeletal Muscle

Article Title: Automated muscle histopathology analysis using CellProfiler

doi: 10.1186/s13395-018-0178-6

Figure Lengend Snippet: Examples of correctly and incorrectly processed muscle images. a Representative pseudo-colored images from all five WT and mdx mice after processed by CellProfiler. Red, centrally nucleated fibers; blue, normal fiber. b An incorrectly processed image with a large black area, which was due to a high threshold setting and can be corrected by lowering the threshold from 0.985 to 0.955. The blue stars showing the inter-fiber spaces that were mistakenly identified as muscle fibers; the blue boxes indicating individual muscle fibers that were mistakenly split into two

Article Snippet: Other requirements: MuscleAnalyzer pipeline requires CellProfiler which is freely available from CellProfiler ( http://cellprofiler.org/ ) developed by the Carpenter Lab at the Broad Institute of Harvard and MIT.

Techniques:

Journal: Skeletal Muscle

Article Title: Automated muscle histopathology analysis using CellProfiler

doi: 10.1186/s13395-018-0178-6

Figure Lengend Snippet: Quantitative measurements of the 67 images processed manually or by CellProfiler. a The average number of muscle fibers per image. b The percentage of CNF. c CSA measurements. d MFD measurements determined by CellProfiler or the manual approach. e Size distribution of WT and mdx muscle fibers generated from the CSA data produced by CellProfiler

Article Snippet: Other requirements: MuscleAnalyzer pipeline requires CellProfiler which is freely available from CellProfiler ( http://cellprofiler.org/ ) developed by the Carpenter Lab at the Broad Institute of Harvard and MIT.

Techniques: Generated, Produced