SV: Could anyone give us a guide about how to use openslide to view WSI

[Thomas Melin]

Hi Mr Gong,
You may find the following links interesting.
Desktop applications:
ASAP: https://github.com/GeertLitjens/ASAP
QuPath: https://qupath.github.io/

Web-based:
Cytomine: https://cytomine.coop/
Pathomation: http://free.pathomation.com/

Best regards,
Thomas Melin
[cid:420a99d5-cdc7-4fe7-9a54-27e37712392d]

Thomas Melin
Senior Development Engineer

ContextVision AB, Storgatan 24, 582 23 Linköping, Sweden
Phone: +46 (0)70 606 85 56
www.contextvision.com<http://www.contextvision.com/>



Från: openslide-users [mailto:openslide-users-bounces+thomas.melin=contextvision.se at lists.andrew.cmu.edu] För Luca Lianas
Skickat: den 23 mars 2018 10:29
Till: Gong, Qi * <Qi.Gong at fda.hhs.gov>
Kopia: openslide-users at lists.andrew.cmu.edu
Ämne: Re: Could anyone give us a guide about how to use openslide to view WSI

Hi Mr Gong and everyone else in the mailing list,
I’m Luca Lianas and I work at the Healthcare Flows group of the CRS4, a research center in Italy.
We’ve been working for a few years now on systems based on Digital Pathology images and, in particular, we developed a tool that can be considered as a plugin for Openmicroscopy’s OMERO (https://www.openmicroscopy.org/omero/) that basically act as a DZI adapter for OME’s platform.
Our plugin, called ome_seadragon (https://www.openmicroscopy.org/omero/) uses both OMERO and OpenSlide and rendering engine for the images and is based on the deepzoom project cited by David de Mena.
The plugin has both the back-end engine to render images in DZI format and the front-end viewer, which is OpenSeadragon, packet as a Javascript library.
The viewer has also drawing utilities developed by using Paper.js which make possible to the user to interact with the image and add 2D graphics on top of that as Regions of Interest.
ome_seadragon is now part of a few projects that we are running over the years, one of them is a e-learning platform called CyTest and if you want to “take a look” to the platform and how the viewer has been integrated with that you can read the publication on Research Gate https://www.researchgate.net/publication/305889225_CyTest_-_An_Innovative_Open-source_Platform_for_Training_and_Testing_in_Cythopathology
I think that ome_seadragon could be considered as a good example on how to use OpenSlide to convert images in DZI format and how to integrate it with an online viewer with ROI marking capabilities.
I hope that my two cents on the discussion were useful.

Best,

Luca Lianas


On 22 Mar 2018, at 17:30, David de Mena <david.mena.exts at juntadeandalucia.es<mailto:david.mena.exts at juntadeandalucia.es>> wrote:

Hi Mr Gong:

There is a python library base on openslide to create deepzoom images: https://github.com/openslide/openslide-python/blob/master/openslide/deepzoom.py Together with a openseadragon (or Googlemaps) JavaScript library you can navigate in the image with a level,x,y.

In an European project called AIDPATH Public Health System of Andalusia have created a DICOM WSI converter/viewer based on this system.

Best
David de Mena García
Responsable de Proyectos de Innovación TIC / ICT Innovation Project Manager
Consejería de Salud de la Junta de Andalucía / Regional Ministry of Health


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El 22 mar 2018, a las 15:51, Gong, Qi * <Qi.Gong at fda.hhs.gov<mailto:Qi.Gong at fda.hhs.gov>> escribió:
Registration accuracy between whole slide images and glass slides in eeDAP workflow
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---

Luca Lianas
Data Intensive Computing - Healthcare Flows
CRS4 - Centro di Ricerche, Sviluppo e Studi Superiori della Sardegna
POLARIS, Edificio 1, 09010 PULA (CA - Italy)
Email: luca.lianas at crs4.it<mailto:luca.lianas at crs4.it>



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