 | | | | | Cursus | | NWI-IMC037 | | Categorie | | MA (Master) | | Voertaal | | Engels | | Aangeboden door | | Radboud Universiteit; Faculteit der Natuurwetenschappen, Wiskunde en Informatica; Informatica en Informatiekunde; | | Docenten | | | | | Collegejaar | | 2022 | | | Periode | | | KW3-KW4 | (30-01-2023 t/m 31-08-2023) |
| | Aanvangsblok | | | KW3 | |
| | Onderwijsvorm | | | voltijd | |
| | Opmerking | | - | | Inschrijven via OSIRIS | | Ja | | Inschrijven voor bijvakkers | | Ja | | Voorinschrijving | | Nee | | Wachtlijst | | Nee | | Plaatsingsprocedure | | - |
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- Learn how basic methods of image processing work
- Learn about important applications in the field of medical image analysis and computer aided diagnosis (CAD)
- Understand the increasing role of machine learning and deep learning in medical imaging
- Design, implement, and evaluate a medical image analysis system for a clinical application
- Learn how to design studies to evaluate medical image analysis systems
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Medical imaging is increasingly gaining importance in medicine. Radiologists use images to detect diseases in an early stage (via screening), to diagnose patients with symptoms, and to monitor the effect of treatment. In pathology digitization of microscopy imaging is just starting, enabling pathologists to use computerized analysis of high-resolution gigapixel images to better diagnose disease in tissue samples. However, as the complexity of imaging (3D/4D) and the amount of data increases the interpretation of images by humans becomes problematic.
Therefore, there is a growing need for intelligent image analysis systems that can aid clinicians with image interpretation and decisions. The goal of these systems is to reproduce visual skills of highly trained human observers and to provide quantitative analysis. For this purpose, machine learning is applied to develop a computer model that can be trained to exploit information from a large number of medical images.
In recent years, Deep Learning [LeCun et al., Nature, 2015] has emerged as the state-of-the-art approach for image analysis applications. While human readers still are superior in most applications, Convolutional Neural Networks have been successfully applied to medical imaging problems like automated reading of mammograms for breast cancer detection, automatic detection of pulmonary nodules for lung cancer screening, detection of breast and prostate cancer in histopathology images and segmentation of white matter lesions in brain magnetic resonance, amongst others, de facto gradually bridging the gap between humans and computers. Finally, recent studies have shown that deep learning algorithms have reached and outperformed human professionals at diagnostic tasks like detection of skin cancer [Esteva et al., Nature, 2017], classification of diabetic retinopathy [Gulshan et al., JAMA, 2016] detection of breast cancer metastasis in lymph nodes [Ehteshami et al., JAMA, 2017], and malignancy risk estimation of lung nodules on CT [Venkadesh et al., Radiology, 2021].
In the first part of the course, students will learn basic concepts of digital image processing, medical imaging, machine learning and deep learning through a series of weekly practical assignments. Lectures and assignments will cover the following topics:
- Introduction to Medical Image Analysis
- Medical Image Processing and Transformation
- Detection, Segmentation and Classification in Medical Imaging
- Machine Learning with Neural Networks
- Deep Learning with Convolutional Neural Networks
- Convolutional Neural Networks and Classification in Medical Imaging
- Convolutional Neural Networks and Segmentation in Medical Imaging
- Convolutional Neural Networks and Detection in Medical Imaging
- Deep Learning for Grand Challenges in Medical Imaging
The second part of the course is dedicated to the development of a CAD system based on deep learning, in the form of a final project, in which small teams of students will apply the concepts and techniques learned in the first part of the course and compete in ongoing grand challenges in medical imaging.
References
- [LeCun et al., Nature, 2015] Yan LeCun, Yoshua Bengio, Geoffrey Hinton, "Deep Learning", Nature, 521, 436–444, 2015
- [Gulshan et al., JAMA, 2016] Varun Gulshan, Lily Peng, Marc Coram, et al., "Development and Validation of a Deep Learning Algorithm for Detection of Diabetic Retinopathy in Retinal Fundus Photographs", JAMA. 2016;316(22):2402-2410
- [Esteva et al., Nature, 2017] Andre Esteva, Brett Kuprel, Roberto A. Novoa, Justin Ko, Susan M. Swetter, Helen M. Blau, Sebastian Thrun, "Dermatologist-level classification of skin cancer with deep neural networks", Nature, 542, 115–11, 2017
- [Ehteshami et al., JAMA, 2017] B. B. Ehteshami et al., "Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer", JAMA. 2017 Dec 12;318(22):2199-2210.
- [Venkadesh et al., Radiology, 2021] K. Venkadesh, A. Setio, A. Schreuder, E. Scholten, K. Chung, M. W Wille, Z. Saghir, B. van Ginneken, M. Prokop and C. Jacobs, "Deep Learning for Malignancy Risk Estimation of Pulmonary Nodules Detected at Low-Dose Screening CT.", Radiology, 2021;300(2):438-447.
Instructional Modes
- Lecture
- Computer practicum
- Self-study
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Knowledge and skills on a level of a BSc in Artificial Intelligence or Computer Science.
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Digital Exam, Recorded presentation, Report.
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Information about research in medical image analysis and computer aided diagnosis at the Radboud University Medical Center can be found at https://www.diagnijmegen.nl. The course will be coordinated by dr. ir. C. Jacobs.
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| | | Aanbevolen materiaalArtikelen| Yann LeCun, Yoshua Bengio and Geoffrey Hinton, Deep Learning, Nature 521, 436–444 (28 May 2015) |
| Artikelen| G. Litjens, T. Kooi, B. Ehteshami Bejnordi, A.A.A. Setio, F. Ciompi, M. Ghafoorian, J. van der Laak, B. van Ginneken and C. Sánchez. "A Survey on Deep Learning in Medical Image Analysis", Medical Image Analysis 2017;42:60-88. |
| Artikelen| Varun Gulshan, Lily Peng, Marc Coram, et al., "Development and Validation of a Deep Learning Algorithm for Detection of Diabetic Retinopathy in Retinal Fundus Photographs", JAMA. 2016;316(22):2402-2410 |
| Artikelen| Andre Esteva, Brett Kuprel, Roberto A. Novoa, Justin Ko, Susan M. Swetter, Helen M. Blau, Sebastian Thrun, "Dermatologist-level classification of skin cancer with deep neural networks", Nature, 542, 115–11, 2017 |
| Artikelen| B. B. Ehteshami et al., "Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer", JAMA. 2017 Dec 12;318(22):2199-2210. |
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WerkvormenCursus
AlgemeenIn the first half of the course basic skills will be developed through a series of lectures and practical assignments. In the second part, a medical image analysis application will be developed in small groups. The topic of this application varies from year to year. Examples are lung nodule detection in CT screening data, detection of diabetic retinopathy in retinal images, and detection of white matter lesions in brain MRI. Applications will be developed in python.
| Project
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ToetsenDigitaal tentamen| Weging | | 2 |
| Toetsvorm | | Digitale toets met CIRRUS |
| Gelegenheden | | Blok KW3, Blok KW4 |
| Eindproject (incl. pres en verslag)| Weging | | 3 |
| Toetsvorm | | Project |
| Gelegenheden | | Blok KW4, Blok KW4 |
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