OpenPhi
OpenPhi provides a standardized programmatic interface to access Philips iSyntax whole-slide images (WSIs) from the Philips Ultra Fast Scanner, enabling interoperable computational analysis and the development of deep-learning-based diagnostic and prognostic methods in digital pathology.
Key Features:
- iSyntax access: Provides programmatic read access to iSyntax-formatted whole-slide images produced by the Philips Ultra Fast Scanner.
- Philips scanner compatibility: Compatible with WSIs produced by the Philips Ultra Fast Scanner (iSyntax).
- Python implementation: Implemented in Python to facilitate integration into analysis pipelines.
- API for computational analysis: Exposes an API for integration into computational-image-analysis and deep-learning workflows for diagnostics and prognostics.
- Dependency on Philips SDK: Requires the Philips Software Development Kit (SDK) for full functionality and access to iSyntax content.
- Interoperability: Enables integration of iSyntax WSIs into vendor-neutral computational applications.
Scientific Applications:
- Deep learning for diagnostics: Supports training and deployment of deep-learning models on iSyntax WSIs for diagnostic tasks.
- Prognostic modeling: Enables development of prognostic algorithms using whole-slide image data.
- Computational pathology algorithm development: Facilitates algorithm development and evaluation on clinical-grade WSI data from the Philips Ultra Fast Scanner.
- Quantitative image analysis: Provides standardized access for quantitative feature extraction and image-based biomarker studies.
Methodology:
Implements a Python API that accesses iSyntax-formatted WSIs via the Philips Software Development Kit (SDK).
Topics
Details
- License:
- MIT
- Cost:
- Free of charge
- Tool Type:
- command-line tool
- Operating Systems:
- Mac, Linux, Windows
- Programming Languages:
- Python
- Added:
- 12/18/2021
- Last Updated:
- 12/18/2021
Operations
Publications
Mulliqi N, Kartasalo K, Olsson H, Ji X, Egevad L, Eklund M, Ruusuvuori P. OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology. Bioinformatics. 2021;37(21):3995-3997. doi:10.1093/bioinformatics/btab578. PMID:34358287. PMCID:PMC8570784.
PMID: 34358287
PMCID: PMC8570784
Funding: - Swedish Research Council: 2019-01466, 2020-00692
- Academy of Finland: 334782, 335976, 341967