title: AutoStitcher: An Automated Program for Efficient and Robust Reconstruction of Digitized Whole Histological Sections from Tissue Fragments.
abstract: In applications involving large tissue specimens that have been sectioned into smaller tissue fragments, manual reconstruction of a "pseudo whole-mount" histological section (PWMHS) can facilitate (a) pathological disease annotation, and (b) image registration and correlation with radiological images. We have previously presented a program called HistoStitcher, which allows for more efficient manual reconstruction than general purpose image editing tools (such as Photoshop). However HistoStitcher is still manual and hence can be laborious and subjective, especially when doing large cohort studies. In this work we present AutoStitcher, a novel automated algorithm for reconstructing PWMHSs from digitized tissue fragments. AutoStitcher reconstructs ("stitches") a PWMHS from a set of 4 fragments by optimizing a novel cost function that is domain-inspired to ensure (i) alignment of similar tissue regions, and (ii) contiguity of the prostate boundary. The algorithm achieves computational efficiency by performing reconstruction in a multi-resolution hierarchy. Automated PWMHS reconstruction results (via AutoStitcher) were quantitatively and qualitatively compared to manual reconstructions obtained via HistoStitcher for 113 prostate pathology sections. Distances between corresponding fiducials placed on each of the automated and manual reconstruction results were between 2.7%-3.2%, reflecting their excellent visual similarity.
authors.affiliation: Case Western Reserve University, Department of Biomedical Engineering, Cleveland OH, 44106, USA.
authors.forename: Gregory
authors.initials: G
authors.lastname: Penzias
authors.affiliation: Case Western Reserve University, Department of Biomedical Engineering, Cleveland OH, 44106, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Janowczyk
authors.affiliation: Case Western Reserve University, Department of Biomedical Engineering, Cleveland OH, 44106, USA.
authors.forename: Asha
authors.initials: A
authors.lastname: Singanamalli
authors.affiliation: Case Western Reserve University, Department of Biomedical Engineering, Cleveland OH, 44106, USA.
authors.forename: Mirabela
authors.initials: M
authors.lastname: Rusu
authors.affiliation: University of Pennsylvania, Department of Pathology, Philadelphia PA, 19104, USA.
authors.forename: Natalie
authors.initials: N
authors.lastname: Shih
authors.affiliation: University of Pennsylvania, Department of Pathology, Philadelphia PA, 19104, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Feldman
authors.affiliation: St. Vincent's Prostate Cancer Clinic, Darlinghurst, NSW, Australia.
authors.forename: Phillip D
authors.initials: PD
authors.lastname: Stricker
authors.affiliation: Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia.
authors.forename: Warick
authors.initials: W
authors.lastname: Delprado
authors.affiliation: Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia.
authors.forename: Sarita
authors.initials: S
authors.lastname: Tiwari
authors.affiliation: Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia.
authors.forename: Maret
authors.initials: M
authors.lastname: Böhm
authors.affiliation: Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia.
authors.forename: Anne-Maree
authors.initials: AM
authors.lastname: Haynes
authors.affiliation: University Hospitals Seidman Cancer Center, Cleveland OH, 44106, USA.
authors.forename: Lee
authors.initials: L
authors.lastname: Ponsky
authors.affiliation: Case Western Reserve University, Department of Biomedical Engineering, Cleveland OH, 44106, USA.
authors.forename: Satish
authors.initials: S
authors.lastname: Viswanath
authors.affiliation: Case Western Reserve University, Department of Biomedical Engineering, Cleveland OH, 44106, USA.
authors.forename: Anant
authors.initials: A
authors.lastname: Madabhushi
mesh_terms: D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D007091:Image Processing, Computer-Assisted; D008279:Magnetic Resonance Imaging; D008297:Male; D010363:Pattern Recognition, Automated / Q000379:methods*; D011467:Prostate / Q000000981:diagnostic imaging* / Q000473:pathology; D011856:Radiographic Image Enhancement / Q000379:methods*