WSIC: a Python package and command-line interface for fast whole slide image conversion.

ABSTRACT

Summary: Whole slide images (WSIs) are multi-gigapixel images of tissue sections, which are used in digital and computational pathology workflows. WSI datasets are commonly heterogeneous collections of proprietary or niche specialized formats which are challenging to handle. This note describes an open-source Python application for efficiently converting between WSI formats, including common, open, and emerging cloud-friendly formats. WSIC is a software tool that can quickly convert WSI files across various formats. It has a high performance and maintains the resolution metadata of the original images. WSIC is ideal for pre-processing large-scale WSI datasets with different file types. Availability and implementation Source code is available on GitHub at https//github.com/John-P/wsic/ under a permissive licence. WSIC is also available as a package on PyPI at https//pypi.org/project/WSIC/.