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

• Published in: MethodsX Vol. 2; no. C; pp. 272 - 277
• Main Authors: Marien, Koen M., Andries, Luc, De Schepper, Stefanie, Kockx, Mark M., De Meyer, Guido R.Y.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2015; Elsevier
• Subjects: Agricultural and Biological Science; Automation; AutoTag and AutoSnap; Computer-assisted image processing; Microvessels; Selection bias; Stereology; Whole slide image; Automation; Whole slide image; AutoTag and AutoSnap; Microvessels; Computer-assisted image processing; Selection bias; Stereology
• ISSN: 2215-0161; 2215-0161
• DOI: 10.1016/j.mex.2015.05.002

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 interest11ROI: region of interest. (ROIs) were selected by manual operations within a tumor by using a systematic uniform random sampling22SURS: 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.