title: Automatic segmentation and quantification of electron micrographs: extracellular components.
abstract: Extracellular glycosaminoglycans when precipitated by tannic acid, appear in electron micrographs as amorphous reticulate masses or fragments sometimes finely beaded and often associated with collagen fibrils. An algorithm for automatic classification, segmentation, and quantification of the amount of tannic acid-precipitable material (TAPM) and collagen in electron microscopic images is presented. Small patches of a region are initially located and the patch boundaries are traced using a binary contour tracing algorithm. The patches are then grown out and merged together to form one large area. This area is classified using a two-dimensional feature vector into one of two classes: a region with TAPM and collagen, or one with cell bodies and/or processes. Once these areas are classified and segmented, the distribution of TAPM is measured. The algorithm was tested on several TAPM images displaying varying amounts and configurations of TAPM with good results. It may also be adapted to process other electron microscopic images containing elements of interest which have complex or amorphous form.
mesh_terms: D000818:Animals; D003094:Collagen / Q000032:analysis; D003201:Computers; D005109:Extracellular Matrix / Q000032:analysis / Q000648:ultrastructure*; D005404:Fixatives; D006025:Glycosaminoglycans / Q000032:analysis*; D006651:Histocytochemistry / Q000379:methods; D047348:Hydrolyzable Tannins; D007089:Image Enhancement / Q000379:methods; D008433:Mathematics; D051379:Mice; D008854:Microscopy, Electron / Q000379:methods; D010159:Palate / Q000196:embryology / Q000648:ultrastructure
chemical_list: D005404:Fixatives; D006025:Glycosaminoglycans; D047348:Hydrolyzable Tannins; D003094:Collagen