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. 2021 Nov 5;37(21):3995-3997.
doi: 10.1093/bioinformatics/btab578.

OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology

Nita Mulliqi  1 , Kimmo Kartasalo  1   2 , Henrik Olsson  1 , Xiaoyi Ji  1 , Lars Egevad  3 , Martin Eklund  1 , Pekka Ruusuvuori  2   4
Affiliations

OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology

Nita Mulliqi et al. Bioinformatics. .

Abstract

Summary: Digital pathology enables applying computational methods, such as deep learning, in pathology for improved diagnostics and prognostics, but lack of interoperability between whole slide image formats of different scanner vendors is a challenge for algorithm developers. We present OpenPhi-Open PatHology Interface, an Application Programming Interface for seamless access to the iSyntax format used by the Philips Ultra Fast Scanner, the first digital pathology scanner approved by the United States Food and Drug Administration. OpenPhi is extensible and easily interfaced with existing vendor-neutral applications.

Availability and implementation: OpenPhi is implemented in Python and is available as open-source under the MIT license at: https://gitlab.com/BioimageInformaticsGroup/openphi. The Philips Software Development Kit is required and available at: https://www.openpathology.philips.com. OpenPhi version 1.1.1 is additionally provided as Supplementary Data.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Left: WSIs contain: (1) a label image for sample identification, (2) a macro image of the glass slide and (3) a multiresolution pyramid of the high-resolution pixel data. OpenPhi provides a compatibility layer, facilitating access to iSyntax WSIs via the Philips SDK, while adhering to a unified API consistent with the OpenSlide Python API. Middle: streamlined access to the images and metadata is provided to developers by a set of high-level methods. Right: applications capable of analyzing WSIs in vendor-neutral manner can be built relying on the unified API.
See this image and copyright information in PMC

References

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