The OMERO.web application to support an image viewer based on OpenSeadragon.

OME Seadragon

The OMERO.web application to support an image viewer based on OpenSeadragon.

Contacts

Challenge

Understanding of organ and tissue structure, at cellular level, is a basic requirement for medical education and demonstration of histological and cytological slides at microscopes are part of the training in medical and biological courses, worldwide. For various reasons, mainly economical, demonstrations at the microscope have in recent times become less practiced, and are encountering difficulties in many Universities. The use of scanned images distributed and commented via Internet (s.c. Virtual Microscope) could overcome the difficulties and result in making histological and cytological examination more popular. A proper setting would be to offer the functionality of a microscope via an interactive application, definite advantages would be the reduced economic cost (compared to the acquirement of several microscopes), the flexibility linked to the fact that clinicians could practice Virtual Microscopy in times and places of preference and even the feeling that this approach could appear "more user friendly", as compared to the technicality of managing a microscope, adjusting view and magnification, focusing etc.

Overview

OME Seadragon is an OMERO.web image viewing application for very high resolution images – like the ones produced by digital pathology scanners – with support for vectorized image-specific regions of interest (ROIs). It is based on the OpenSeadragon viewer and paper.js framework.

Innovative features

  • the web application acts like a middleware between OMERO.server and our viewer;
  • it converts images to DZI (Deep Zoom Image) format (XML specification defined and maintained by Microsoft);
  • the conversion process is carried on by different engines that can be configured by the user;
  • currently, we support rendering based on the openslide library (Goode at al., 2013) and on OMERO rendering libraries (which do not support DZI format natively) making OME Seadragon a DZI format wrapper for OMERO.

Potential users

Researchers, developers

Impact sectors

Health - ICT - digital pathology

Other resources

  1. https://github.com/crs4/ome_seadragon
  2. https://github.com/crs4/ome_seadragon_cache
  3. https://github.com/crs4/ome_seadragon_gateway
  4. L. Lianas, M. E. Piras, E. Musu, S. Podda, F. Frexia, E. Ovcin, G. Bussolati, G. Zanetti, CyTest - A new platform for training and testing in cytopathology. The Diagnostic pathology Journal, Volume 2, page 208 - august 2016.
  5. L. Lianas, M. E. Piras, E. Musu, S. Podda, F. Frexia, E. Ovcin, G. Bussolati, G. Zanetti, CyTest – An Innovative Open-source Platform for Training and Testing in Cythopathology. Procedia - Social and Behavioral Sciences, Volume 228, page 674–681 - july 2016.

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