Tag Archives: HistoQC

The noise in our digital pathology slides

In adding new features to HistoQC , I stumbled upon a very interesting insight that I thought I would take a moment to share. The amount of noise and artifacts in digital pathology (DP) whole slide images (WSI) is far more extensive than I had previously thought.

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Converting an existing image into an Openslide compatible format

Many digital pathology tools (e.g., our quality control tool, HistoQC), employ Openslide, a library for reading whole slide images (WSI).  Openslide provides a reliable abstraction away from a number of proprietary WSI file-formats, such that a single programmatic interface can be employed to access WSI meta and image data.

Unfortunately, when smaller regions of interest, or new images, are created in tif/png/jpg formats they no longer remain compatible with OpenSlide. This blog post discusses how to take any image and convert it into an OpenSlide compatible WSI, with embedded metadata.

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