title: Framework for parsing, visualizing and scoring tissue microarray images.
abstract: Increasingly automated techniques for arraying, immunostaining, and imaging tissue sections led us to design software for convenient management, display, and scoring. Demand for molecular marker data derived in situ from tissue has driven histology informatics automation to the point where one can envision the computer, rather than the microscope, as the primary viewing platform for histopathological scoring and diagnoses. Tissue microarrays (TMAs), with hundreds or even thousands of patients' tissue sections on each slide, were the first step in this wave of automation. Via TMAs, increasingly rapid identification of the molecular patterns of cancer that define distinct clinical outcome groups among patients has become possible. TMAs have moved the bottleneck of acquiring molecular pattern information away from sampling and processing the tissues to the tasks of scoring and results analyses. The need to read large numbers of new slides, primarily for research purposes, is driving continuing advances in commercially available automated microscopy instruments that already do or soon will automatically image hundreds of slides per day. We reviewed strategies for acquiring, collating, and storing histological images with the goal of streamlining subsequent data analyses. As a result of this work, we report an implementation of software for automated preprocessing, organization, storage, and display of high resolution composite TMA images.
authors.affiliation: Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA. amrabino@ucsd.edu
authors.forename: Andrew
authors.initials: A
authors.lastname: Rabinovich
authors.forename: Stan
authors.initials: S
authors.lastname: Krajewski
authors.forename: Maryla
authors.initials: M
authors.lastname: Krajewska
authors.forename: Ahmed
authors.initials: A
authors.lastname: Shabaik
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Hewitt
authors.forename: Serge
authors.initials: S
authors.lastname: Belongie
authors.forename: John C
authors.initials: JC
authors.lastname: Reed
authors.forename: Jeffrey H
authors.initials: JH
authors.lastname: Price
mesh_terms: D003581:Cytodiagnosis / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D006651:Histocytochemistry / Q000379:methods*; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D046228:Microarray Analysis / Q000379:methods*; D008853:Microscopy / Q000379:methods*; D012984:Software; D046509:Tissue Culture Techniques / Q000379:methods; D014584:User-Computer Interface