title: CognitionMaster: an object-based image analysis framework.
abstract: BACKGROUND
  Automated image analysis methods are becoming more and more important to extract and quantify image features in microscopy-based biomedical studies and several commercial or open-source tools are available. However, most of the approaches rely on pixel-wise operations, a concept that has limitations when high-level object features and relationships between objects are studied and if user-interactivity on the object-level is desired.
  
  
  RESULTS
  In this paper we present an open-source software that facilitates the analysis of content features and object relationships by using objects as basic processing unit instead of individual pixels. Our approach enables also users without programming knowledge to compose "analysis pipelines" that exploit the object-level approach. We demonstrate the design and use of example pipelines for the immunohistochemistry-based cell proliferation quantification in breast cancer and two-photon fluorescence microscopy data about bone-osteoclast interaction, which underline the advantages of the object-based concept.
  
  
  CONCLUSIONS
  We introduce an open source software system that offers object-based image analysis. The object-based concept allows for a straight-forward development of object-related interactive or fully automated image analysis solutions. The presented software may therefore serve as a basis for various applications in the field of digital image analysis.
authors: Institute of Pathology, Charité University Hospital Berlin, Charitéplatz 1, Berlin, 10117, Germany. frederick.klauschen@charite.de
authors: Stephan
authors: S
authors: Wienert
authors: Daniel
authors: D
authors: Heim
authors: Manato
authors: M
authors: Kotani
authors: Björn
authors: B
authors: Lindequist
authors: Albrecht
authors: A
authors: Stenzinger
authors: Masaru
authors: M
authors: Ishii
authors: Peter
authors: P
authors: Hufnagl
authors: Michael
authors: M
authors: Beil
authors: Manfred
authors: M
authors: Dietel
authors: Carsten
authors: C
authors: Denkert
authors: Frederick
authors: F
authors: Klauschen
mesh_terms: D000465:Algorithms; D057205:Automation, Laboratory; D001842:Bone and Bones / Q000473:pathology*; D001943:Breast Neoplasms / Q000737:chemistry / Q000473:pathology*; D002450:Cell Communication; D049109:Cell Proliferation; D005260:Female; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D007150:Immunohistochemistry / Q000379:methods*; D019394:Ki-67 Antigen / Q000032:analysis; D036641:Microscopy, Fluorescence, Multiphoton / Q000379:methods*; D010010:Osteoclasts / Q000473:pathology*; D011237:Predictive Value of Tests; D012984:Software
chemical_list: D019394:Ki-67 Antigen