title: TMARKER: A free software toolkit for histopathological cell counting and staining estimation.
abstract: BACKGROUND
  Histological tissue analysis often involves manual cell counting and staining estimation of cancerous cells. These assessments are extremely time consuming, highly subjective and prone to error, since immunohistochemically stained cancer tissues usually show high variability in cell sizes, morphological structures and staining quality. To facilitate reproducible analysis in clinical practice as well as for cancer research, objective computer assisted staining estimation is highly desirable.
  
  
  METHODS
  We employ machine learning algorithms as randomized decision trees and support vector machines for nucleus detection and classification. Superpixels as segmentation over the tissue image are classified into foreground and background and thereafter into malignant and benign, learning from the user's feedback. As a fast alternative without nucleus classification, the existing color deconvolution method is incorporated.
  
  
  RESULTS
  Our program TMARKER connects already available workflows for computational pathology and immunohistochemical tissue rating with modern active learning algorithms from machine learning and computer vision. On a test dataset of human renal clear cell carcinoma and prostate carcinoma, the performance of the used algorithms is equivalent to two independent pathologists for nucleus detection and classification.
  
  
  CONCLUSIONS
  We present a novel, free and operating system independent software package for computational cell counting and staining estimation, supporting IHC stained tissue analysis in clinic and for research. Proprietary toolboxes for similar tasks are expensive, bound to specific commercial hardware (e.g. a microscope) and mostly not quantitatively validated in terms of performance and reproducibility. We are confident that the presented software package will proof valuable for the scientific community and we anticipate a broader application domain due to the possibility to interactively learn models for new image types.
authors.affiliation: Institute for Computational Science, ETH Zurich, Switzerland ; Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, Switzerland.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Schüffler
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Fuchs
authors.forename: Cheng Soon
authors.initials: CS
authors.lastname: Ong
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Wild
authors.forename: Niels J
authors.initials: NJ
authors.lastname: Rupp
authors.forename: Joachim M
authors.initials: JM
authors.lastname: Buhmann
keywords: Color deconvolution; nuclei detection; pathology; segmentation staining estimation; superpixel classification