Automated macrophage counting in DLBCL tissue samples: a ROF filter based approach


We describe a Rudin-Osher-Fatemi (ROF) filter based segmentation approach for whole tissue samples, combining floating intensity thresholding and rule-based feature detection. Method is validated against manual counts and compared with two commercial software kits (Tissue Studio 64, Definiens AG, and Halo, Indica Labs) and a straightforward machine-learning approach in a set of 50 test images. Further, the novel method and both commercial packages are applied to a set of 44 whole tissue sections. Outputs are compared with gene expression data available for the same tissue samples. Finally, the ROF based method is applied to 44 expert-specified tumor subregions for testing selection and subsampling strategies.

Our method is deterministic, fully automated, externally repeatable, independent on training data and -- in difference to most commercial software kits -- completely documented. Among all tested methods, the novel approach is best correlated with manual count (0.9297). Automated detection of evaluation subregions proved to be fully reliable. Subsampling within tumor subregions is possible with results almost identical to full sampling. Comparison with gene expression data obtained for the same tissue samples reveals only moderate to low correlation levels, thus indicating that image morphometry constitutes an independent source of information about antibody-polarized macrophage occurence and distribution.

DOI: 10.1186/s12575-019-0098-9

Projects: MMML Demonstrators - Molecular Mechanisms in Malignant Lymphomas - Demon...

Publication type: Not specified

Journal: Biological Procedures Online

Human Diseases: Diffuse large b-cell lymphoma


Date Published: No date defined

Registered Mode: Not specified

Authors: Marcus Wagner, René Hänsel, Sarah Reinke, Julia Richter, Michael Altenbuchinger, Ulf-Dietrich Braumann, Rainer Spang, Markus Löffler, Wolfram Klapper

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Wagner, M., Hänsel, R., Reinke, S., Richter, J., Altenbuchinger, M., Braumann, U.-D., Spang, R., Löffler, M., & Klapper, W. (2019). Automated macrophage counting in DLBCL tissue samples: a ROF filter based approach. In Biological Procedures Online (Vol. 21, Issue 1). Springer Science and Business Media LLC.

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Created: 27th May 2019 at 07:40

Last updated: 7th Dec 2021 at 17:58

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