omero matlab toolbox  (MathWorks Inc)

Journal: Diagnostic Pathology

Article Title: Automatic evaluation of tumor budding in immunohistochemically stained colorectal carcinomas and correlation to clinical outcome

doi: 10.1186/s13000-018-0739-3

Figure Lengend Snippet: Sketch of the analysis. A) ROI tumor (not shown) and the ROI border (dashed red line) were manually delineated by a pathologist (CW). A1: a sliding window moved over the ROI border and cropped every half TMA diameter in the underlying, TMA core-sized image. A2: The resulting tile (exactly the size of one TMA core) was then defined as a virtual TMA (vTMA). b , c This procedure leads to a value (number of tumor buds or budding score) per vTMA. This spatial data could be plotted as a heat map (example heat maps with arbitrary values in the left part) or as a histogram (right part of the figure)

Article Snippet: Subsequently, all grid points within the above specified ROI were loaded on the basis of the Omero-MATLAB-toolbox and saved as a TMA core object (containing the slide ID, the core name and position, and an IHC image of the core).

Techniques:

Journal: Diagnostic Pathology

Article Title: Automatic evaluation of tumor budding in immunohistochemically stained colorectal carcinomas and correlation to clinical outcome

doi: 10.1186/s13000-018-0739-3

Figure Lengend Snippet: Definition and detection of tumor buds. a Example single TMA core stained for pan-cytokeratin and hematoxylin and eosin (HE). The red circle highlights a tumor bud next to larger tumor island. The blue circle is a small tumor part, which we referred to as a “tumor islet”; which is a small tumor aggregate but does not meet all criteria for a tumor bud. b Histogram of pan-cytokeratin positive tumor area per core (upper plot) and pan-cytokeratin tumor bud area per core (lower plot). One can see that the mean area of all tumor fragments (upper panel) shows a huge dispersion (x-axis 0–100,000), whereas the mean area of the tumor buds is less distributed (x-axis 0–1000)

Article Snippet: Subsequently, all grid points within the above specified ROI were loaded on the basis of the Omero-MATLAB-toolbox and saved as a TMA core object (containing the slide ID, the core name and position, and an IHC image of the core).

Techniques: Staining, Dispersion