1, 2). Examples include trichrome for fibrosis9 or absence of staining for fat.17 Pixel-based analyses are powerful, but unable to easily provide information about cell-specific physical

characteristics (size, shape, location) or complex data from multiple analytes, or social interactions. Common open source software (e.g., ImageJ) is rich in functionality for routinely captured static images but does not easily accommodate WSI. Cell-based image analysis (e.g., FARSIGHT and IAE-NearCYTE) is a higher-level image analysis approach based on grouping of similarly colored pixels into biologically meaningful structures, such as cells and/or parts selleck products thereof. Each nucleus can serve as the nidus for cell-associated nuclear and/or

cytoplasmic analyte(s) (protein, DNA, mRNA) assays (Supporting Fig. 3). This enables identification of complex specific cell types based on Boolean logic relationships among Selleck Dinaciclib multiple characteristics. For example, hepatocytes can be identified as cells with a relatively large (>23 μm2) round nucleus surrounded by β-catenin staining within a distance of 10 μm from the nucleus and negative CK19 staining (i.e., β-cateninfar/CK19-), whereas BECs are defined as smaller CK19+ cells. Cell-based approaches also enable the collection of data regarding location (X,Y) for 2D thin sections and Z planar addresses for thick sections, nuclear and cytoplasmic physical attributes (e.g., size, shape, and orientation characteristics), and nuclear and/or cytoplasmic analyte expression. Data collection can be followed by more sophisticated queries of social relationship. Cell-based approaches also enable “tissue-tethered cytometry.” This refers to an ability to “virtually digest” the WSI. Each cell, regardless of size, shape, location, or phenotypic complexity, can be isolated and displayed in various formats. Examples include traditional and multidimensional

scatterplots, whiskerplots, and signaling pathway schemes derived Decitabine mw from covariance relationships (data not shown). Importantly, individual cells in either scatterplots or WSI are tethered to the exact same cell on the complementary display. The observer can easily transition between displays to assess the cell from informational perspectives. To distinguish between the two approaches, 10 portal tracts and 10 perivenular ROIs were selected randomly from panel A (CK19/β-catenin/CD31/αSMA/DAPI)-stained high-resolution (40×) WSI images to determine the relative proportions of cell types in two separate livers (Supporting Table 1, Supporting Fig. 1A,B). As expected, αSMA+ cells were overrepresented and BECs were found only in portal/periportal ROIs compared to perivenular regions. FARSIGHT-generated data for hepatocytes, BEC, endothelial cell (EC), and smooth muscle cell (SMC) (Fig. 1A) sorted from one liver (total 20 ROIs) yielded 539/18,875 (2.86%) BECs; 9,153/18,875 (48.5%) hepatocytes; 1,093/18,875 (5.79%) EC; 669/18,875 (3.