Infrastructure Tools

The infrastructure group is part of the Biomedical Imaging Group Rotterdam (BIGR) and Radiology and Nuclear Medicine at the Erasmus MC. We develop software and solutions for large scale image analysis problems with a focus on reproducibility, flexibility and quality. We have a user centric approach and we work directly together with the end-users and partners in creating the best possible solutions.

Working closely together with the Rotterdam Scan Study, Radiologists and doing image analysis research on large datasets resulted in solid expertise on how to deal with large amounts of data and how to streamline the processes around research on large scale data-sets. The team comprises decades of experience in doing medical image analysis research and Research Software Engineering.

We are mainly funded by research infrastructure projects both national and international. We participate actively in national and international communities and sharing knowledge is part of our core vision. We are strong believers in Open Source, most of our infrastructure components are licensed under the Apache 2.0 license. We welcome contributions and collaboration requests.

Team

Contact

Please contact Marcel Koek for questions and inquiries about our solutions.

Publications

Journal Articles

  1. Vernooij, M. W., Jasperse, B., Steketee, R., Koek, M., Vrooman, H., Ikram, M. A., … Niessen, W. J. (2018). Automatic normative quantification of brain tissue volume to support the diagnosis of dementia: A clinical evaluation of diagnostic accuracy. NeuroImage: Clinical, 20, 374–379.
  2. Steketee, R., Vernooij, M. W., Jasperse, B., Koek, M., Vrooman, H. A., Ikram, M. A., … others. (2017). AUTOMATIC QUANTIFICATION OF BRAIN MRI TO IMPROVE THE DIAGNOSTIC WORKUP OF DEMENTIA IN MEMORY CLINIC PATIENTS. Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association, 13(7), P1119–P1120.
  3. Achterberg, H. C., Koek, M., & Niessen, W. J. (2016). Fastr: A workflow engine for advanced data flows in medical image analysis. Frontiers in ICT, 3, 15.
  4. Riba-Llena, I., Koek, M., Verhaaren, B. F. J., Vrooman, H. A., van der Lugt, A., Hofman, A., … Vernooij, M. W. (2015). Small cortical infarcts: prevalence, determinants, and cognitive correlates in the general population. International Journal of Stroke, 10, 18–24.

Conference Articles

  1. Klein, S., Vast, E., Van Soest, J., Dekker, A., Koek, M., & Niessen, W. (2015). XNAT imaging platform for BioMedBridges and CTMM TraIT. In Journal of clinical bioinformatics (Vol. 5, p. S18). BioMed Central.
  2. Koek, M., Achterberg, H., de Groot, M., Vast, E., Klein, S., & Niessen, W. (2015). Population Imaging Study IT Infrastructure: An Automated Continuous Workflow Approach. In 1 st MICCAI Workshop on (p. 31).
  3. Achterberg, H., Koek, M., & Niessen, W. (2015). Fastr: a workflow engine for advanced data flows. In 1st MICCAI Workshop on Management and Processing of Images for Population Imaging (Munich) (pp. 39–46).
  4. De Boer, P., Ranguelova, E., Ivanova, M., Koek, M., Van Der Lijn, F., Niessen, W., … others. (2013). eScience Infrastructure for sharing neuroimaging data and running validated analysis pipelines on a high performance cloud. In Front. Neuroinform. Conference Abstract: Neuroinformatics.
  5. Niessen, W., Vrooman, H., de Boer, R., van der Lijn, F., Achterberg, H., Koek, M., … others. (2012). Quantitative imaging biomarkers in neurologic disease: Population study perspective. In 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI) (pp. 911–911). IEEE.
  6. Vrooman, H. A., Jasperse, M. M. S., Koek, M., van der Lijn, F., Achterberg, H. C., de Bruijne, M., … Niessen, W. J. (2011). A computer-aided diagnosis system for the early and differential diagnosis of neurodegenerative disease. In European Congress of Radiology.