tissue

require(mzkit);

#' tools for HE-stain image analysis
imports "tissue" from "mzplot";

tools for HE-stain image analysis Pathology is practiced by visual inspection of histochemically stained tissue slides. While the hematoxylin and eosin (H&E) stain is most commonly used, special stains can provide additional contrast to different tissue components. Histological analysis of stained human tissue samples is the gold standard for evaluation of many diseases, as the fundamental basis of any pathologic evaluation is the examination of histologically stained tissue affixed on a glass slide using either a microscope or a digitized version of the histologic image following the image capture by a whole slide image (WSI) scanner. The histological staining step is a critical part of the pathology workflow and is required to provide contrast and color to tissue by facilitating a chromatic distinction among different tissue constituents. The most common stain (otherwise referred to as the routine stain) is the hematoxylin and eosin (H&E), which is applied to nearly all clinical cases, covering ~80% of all the human tissue staining performed globally1. The H&E stain is relatively easy to perform and is widely used across the industry. In addition to H&E, there are a variety of other histological stains with different properties which are used by pathologists to better highlight different tissue constituents.