Two papers from Radboudumc have been accepted for oral presentation at the SPIE conference on Digital Pathology, which will be held in February 2021 in San Diego. The abstracts are available here.
Neural image compression for non-small cell lung cancer subtype classification in H&E stained whole-slide images
Author(s): Witali Aswolinskiy, David Tellez, Gabriel Raya, Lieke van der Woude, Monika Looijen-Salamon, Jeroen van der Laak, Katrien Grünberg, Francesco Ciompi, Radboud Univ. Medical Ctr. (Netherlands)
This paper addresses the problem of lung cancer classification, which is one of the topics of ExaMode, and uses whole-slide image compression, which is a technology that is being developed in the project.
Few-shot weakly supervised detection and retrieval in histopathology whole-slide images
Author(s): Mart van Rijthoven, Maschenka Balkenhol, Radboud Univ. Medical Ctr. (Netherlands); Manfredo Atzori, Haute Ecole Spécialisée de Suisse Occidentale (Switzerland); Peter Bult, Radboud Univ. Medical Ctr. (Netherlands); Jeroen van der Laak, Radboud Univ. Medical Ctr. (Netherlands), Linköping Univ. (Sweden); Francesco Ciompi, Radboud Univ. Medical Ctr. (Netherlands)
The second paper contains work from Deliverable D4.1, and it is in collaboration with HES-SO.
Congratulations to Sebastian Otálora, Niccolò Marini, Henning Müller, and Manfredo Atzori who received the “People’s choice award” at the MICCAI 2020 LABELS Workshop (Large-scale Annotation of Biomedical data and Expert Label Synthesis).
The article entitled “The Semi-weakly Supervised Learning for Prostate Cancer Image Classification with Teacher-Student Deep Convolutional Networks” is available at the following link: https://link.springer.com/chapter/10.1007%2F978-3-030-61166-8_21
MicroscopeIT has just finished the first prototype of Virtum, a digital histopathology-dedicated application developed as one of the prototypes in the ExaMode project.
This innovative solution is based on MicroscopeIT’s proprietary Virtum Technology which includes, inter alia, pre-developed modules for storage, management, sharing, processing, and annotating image data, such as Whole Slide Images (WSIs) and other types of biomedical data.
Virtum HP is a digital histopathology-dedicated cloud-based application with virtually unlimited storage and computational resources and can be used to build customized image-analysis applications with integrated AI models.
For more information, you can look at the YouTube video or contact directly MicroscopeIT
UNIPD updated the ExaMode ontology online on Zenodo, by adding the remaining diseases. Now the ontology describes colon carcinoma, lung carcinoma, cervix carcinoma, and the coeliac disease. The ontology documentation is available here, while the Zenodo page is accessible at the following link:
September 9 2020 the ExaMode team went through the Periodic Report of the project for month 18. The report showed the results of the team and the high-quality results achieved so far. The collaboration among the partners is being fruitful, driving technical partners to solve practical clinical needs with a variety of advanced methods, expertise, and knowledge from different domains. All deliverables were accepted.
Sirma AI (Ontotext) will deliver a webinar for Examode through BDVA.
The webinar, scheduled on the 2nd of July 2020, 2 PM CEST, is free but for the live session is required a registration.
The webinar will be recorded and will be available as a free video for those who are unable to attend the live session.
The agenda of the webinar includes:
- Objectives of the ExaMode project
- Knowledge management of diagnosis-related medical data using advanced text analytical technologies and knowledge graphs.
- Demonstration of services:
• Advanced text analytics for semantic data normalization of Electronic Health Record (EHR) extracts – clinical synopsis
• Semantic data fusion of extracted results with a referential knowledge graph built from relevant ontologies and thesauri (Mondo Disease Ontology, Disease Ontology, UMLS, SNOMED-CT, and others)
• Visual graph analytics and exploration of semantically normalized cases in the context of the referential knowledge graph
• Graph similarity search for the identification of similar medical cases
The solution is implemented on top of Ontotext’s GraphDB, a highly scalable RDF triple store.
We release the first version of the ExaMode OWL 2 Ontology. The ontology can also be accessed through Zenodo or downloaded directly here (ttl format).
The ExaMode project was added to the 28th Symposium on Advanced Database Systems (SEBD2020) projects dissemination webpage.
Read here the Facebook AI Research (FAIR) blog post on the collaboration between Radboud University Medical Center (Nijmegen, Netherlands), FAIR (Montreal, Canada) and Erasmus Medical Center (Rotterdam, Netherlands) on histopathology whole-slide image classification using whole-slide image compression with Neural Image Compression and Multitask learning, with application to prediction of a genetic score in breast cancer and patient outcome in colorectal cancer metastasis to the liver.
The work is related to the paper “Extending Unsupervised Neural Image Compression With Supervised Multitask Learning“.
The fourth ExaMode meeting was held on Zoom due to the COVID19 emergency, 4-5th of June 2020.
We are in the 18th month of the project. Over 80% of the tasks have already started. We completed 5 out of 10 milestones. By the end of June, we’ll have 24 out of 49 deliverables ready. So far, the project resulted in 27 scientific papers accepted, and another 9 are currently being evaluated.