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

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 interest (ROIs) were selected by manual operations within a tumor by using a 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.