MethodsX (Jan 2015)

AutoTag and AutoSnap: Standardized, semi-automatic capture of regions of interest from whole slide images

  • Koen M. Marien,
  • Luc Andries,
  • Stefanie De Schepper,
  • Mark M. Kockx,
  • Guido R.Y. De Meyer

DOI
https://doi.org/10.1016/j.mex.2015.05.002
Journal volume & issue
Vol. 2, no. C
pp. 272 – 277

Abstract

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Tumor angiogenesis is measured by counting microvessels in tissue sections at high power magnification as a potential prognostic or predictive biomarker. Until now, regions of interest1 1 ROI: region of interest. (ROIs) were selected by manual operations within a tumor by using a systematic uniform random sampling 2 SURS: systematic, uniform random sampling. (SURS) approach. Although SURS is the most reliable sampling method, it implies a high workload. However, SURS can be semi-automated and in this way contribute to the development of a validated quantification method for microvessel counting in the clinical setting. Here, we report a method to use semi-automated SURS for microvessel counting: • Whole slide imaging with Pannoramic SCAN (3DHISTECH) • Computer-assisted sampling in Pannoramic Viewer (3DHISTECH) extended by two self-written AutoHotkey applications (AutoTag and AutoSnap) • The use of digital grids in Photoshop® and Bridge® (Adobe Systems) This rapid procedure allows traceability essential for high throughput protein analysis of immunohistochemically stained tissue.

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