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An imaging workflow for characterizing phenotypical change in large histological mouse model datasets.

Motivation: This paper presents a workflow designed to quantitatively characterize the 3D structural attributes of macroscopic tissue specimens acquired at a micron level resolution using light microscopy. The specific application is a study of the morphological change in a mouse placenta induced by...

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Published in:Journal of Biomedical Informatics Vol. 41; no. 6; pp. 863 - 874
Main Authors: Mosaliganti K, Pan T, Ridgway R, Sharp R, Cooper L, Gulacy A, Sharma A, Irfanoglu O, Machiraju R, Kurc T, Bruin A, Wenzel P, Leone G, Saltz J, Huang K, Mosaliganti, Kishore, Pan, Tony, Ridgway, Randall, Sharp, Richard, Cooper, Lee
Format: research Journal Article
Published: Academic Press Inc. Dec2008
Online Access:View this record in EBSCOhost
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      jtl: Journal of Biomedical Informatics
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    pubinfo:
      dt: Dec2008
      vid: 41
      iid: 6
      pid: 735
      pub: Academic Press Inc.
      place: Burlington, Massachusetts
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        105574724
        NLM18502696
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        10.1016/j.jbi.2008.03.013
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        105574724
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        atl: An imaging workflow for characterizing phenotypical change in large histological mouse model datasets.
      aug:
        au:
          Mosaliganti K
          Pan T
          Ridgway R
          Sharp R
          Cooper L
          Gulacy A
          Sharma A
          Irfanoglu O
          Machiraju R
          Kurc T
          Bruin A
          Wenzel P
          Leone G
          Saltz J
          Huang K
          Mosaliganti, Kishore
          Pan, Tony
          Ridgway, Randall
          Sharp, Richard
          Cooper, Lee
        affil: Department of Biomedical Informatics, The Ohio State University, 3190 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, USA
      sug:
        subj:
          Models, Biological
          Algorithms
          Animals
          Female
          Image Processing, Computer Assisted
          Mice
          Oncogenes
          Placenta Anatomy and Histology
          Female
      ab: Motivation: This paper presents a workflow designed to quantitatively characterize the 3D structural attributes of macroscopic tissue specimens acquired at a micron level resolution using light microscopy. The specific application is a study of the morphological change in a mouse placenta induced by knocking out the retinoblastoma gene.Result: This workflow includes four major components: (i) serial section image acquisition, (ii) image preprocessing, (iii) image analysis involving 2D pair-wise registration, 2D segmentation and 3D reconstruction, and (iv) visualization and quantification of phenotyping parameters. Several new algorithms have been developed within each workflow component. The results confirm the hypotheses that (i) the volume of labyrinth tissue decreases in mutant mice with the retinoblastoma (Rb) gene knockout and (ii) there is more interdigitation at the surface between the labyrinth and spongiotrophoblast tissues in mutant placenta. Additional confidence stem from agreement in the 3D visualization and the quantitative results generated.Availability: The source code is available upon request.
      pubtype: Academic Journal
      doctype:
        research
        Journal Article
      ougenre: Article
    language: English
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