Blog Post: Quantifying H&E Slide Images: Converting SVS File Format

At Visikol, we deliver best-in-class digital pathology solutions for clients and have a strong focus on shifting the paradigm of pathology from a qualitative to quantitative approach. In order to perform proper quantitative image processing, it is important to have files of the right type whereas many files types are incompatible with image processing software (e.g. ImageJ). Many of the proprietary software programs associated with imaging instrumentation like confocal microscopes, slide scanners, and high-content screening platforms often output raw image files with their own custom formats that are frequently based on the already widely used standard image file formats (such as TIFF), but with custom tags added for storing metadata.

One common instance of this occurrence is in the output of digital slide scanners, such as the Aperio series available from Leica. These are commonly used imaging platforms for digitizing glass slide-mounted tissues sections stained with H&E or for IHC, and the raw images generated are output as .svs files, which contain the full resolution tiff in addition to a thumbnail, a slide label, and one or more pyramid images of lower magnification where applicable. Although the output files can be easily opened and viewed with software like ImageScope, there may be a need for additional processing and quantification that is not readily performed in that software.

In order to extract a high-quality image though, one needs better than a snapshot view, which will not save the full resolution available. For this, one can use the “Export Images” option in ImageScope which is available in the file menu, or on the standard toolbar there is an option for “Extract Region”, which gives the added benefit of choosing the file type output – be it tif, jpeg, or other – and one can select the compression ratio, which will allow for precise control over file size, which can be considerable in some cases. These files can then be opened in a more standard image viewing and processing program, like ImageJ, with the aid of the BioFormats Importer Plugin. This conversion approach allows .svs files to be easily convertd into .tiff files but is ultimately a low throughput/manual approach. If interested in high-throughput digital pathology analysis please reach out to our team at info@visikol.com

Author: Dr. Graeme Gardner

Michael Johnson