title: Structure-Preserving Color Normalization and Sparse Stain Separation for Histological Images.
abstract: Staining and scanning of tissue samples for microscopic examination is fraught with undesirable color variations arising from differences in raw materials and manufacturing techniques of stain vendors, staining protocols of labs, and color responses of digital scanners. When comparing tissue samples, color normalization and stain separation of the tissue images can be helpful for both pathologists and software. Techniques that are used for natural images fail to utilize structural properties of stained tissue samples and produce undesirable color distortions. The stain concentration cannot be negative. Tissue samples are stained with only a few stains and most tissue regions are characterized by at most one effective stain. We model these physical phenomena that define the tissue structure by first decomposing images in an unsupervised manner into stain density maps that are sparse and non-negative. For a given image, we combine its stain density maps with stain color basis of a pathologist-preferred target image, thus altering only its color while preserving its structure described by the maps. Stain density correlation with ground truth and preference by pathologists were higher for images normalized using our method when compared to other alternatives. We also propose a computationally faster extension of this technique for large whole-slide images that selects an appropriate patch sample instead of using the entire image to compute the stain color basis.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Vahadane
authors.forename: Tingying
authors.initials: T
authors.lastname: Peng
authors.forename: Amit
authors.initials: A
authors.lastname: Sethi
authors.forename: Shadi
authors.initials: S
authors.lastname: Albarqouni
authors.forename: Lichao
authors.initials: L
authors.lastname: Wang
authors.forename: Maximilian
authors.initials: M
authors.lastname: Baust
authors.forename: Katja
authors.initials: K
authors.lastname: Steiger
authors.forename: Anna Melissa
authors.initials: AM
authors.lastname: Schlitter
authors.forename: Irene
authors.initials: I
authors.lastname: Esposito
authors.forename: Nassir
authors.initials: N
authors.lastname: Navab
mesh_terms: D003116:Color; D004396:Coloring Agents / Q000737:chemistry*; D008853:Microscopy; D012984:Software; D013194:Staining and Labeling
chemical_list: D004396:Coloring Agents