Research

Background:

Approximately 7,400 women are diagnosed with ovarian cancer every year in the UK [1] and 300,000 worldwide [2]. Medical imaging is routinely used for diagnosis and treatment monitoring of patients with solid tumours and is currently the only available technique for noninvasively assessing treatment response taking into account the overall tumour burden and its spatial and temporal heterogeneity, which in turn are associated with outcome [3]. Currently, image segmentation and evaluation are mostly performed manually and semiquantitatively. The advent of modern computing and the availability of large digital image databanks have led to development of quantitative, data-driven, machine-learning-based medical image analysis methods (radiomics) which have shown great promise in facilitating a deeper understanding of tumour biology, capturing tumour heterogeneity and monitoring tumour evolution and therapy response [4-6]. However, the robustness and generalisability of the radiomics results depend on standardisation of CT instrumentation, data acquisition protocols, choice of reconstruction algorithm, pixel size, etc. [6, 7] which typically vary widely in routine clinical practice.

Outcomes and Impact:

Our project addresses the above challenges and provides a robust image analysis pipeline that improves significantly on the performance and predictive power of current radiomics metrics, ultimately improving clinical decisions and patient outcomes:

  • It exploits the power of novel deep neural networks to produce uniform and homogeneous images.

  • It seamlessly integrates image reconstruction with subsequent steps like semantic segmentation (pixel-wise classification) and radiomics analysis.

  • It is integrated in patient’s clinical workflow, providing accurate dynamic quantification of tumour burden that can be used to make real time treatment decisions in both the clinic and MDT settings.

  1. https://www.cancerresearchuk.org/health-professional/cancer-statistics/statistics-by-cancertype/ovarian-cancer#heading-Zero, Accessed November 2018
  2. Ferlay J, Ervik M, Lam F, Colombet M, Mery L, Piñeros M, Znaor A, Soerjomataram I, Bray F (2018). Global Cancer Observatory: Cancer Today. Lyon, France: International Agency for Research on Cancer. Available from: https://gco.iarc.fr/today, accessed November 2018.
  3. Vargas HA, Veeraraghavan H, Micco M, Nougaret S, Lakhman Y, Meier AA, Sosa R, Soslow RA, Levine DA, Weigelt B, Aghajanian C, Hricak H, Deasy J, Snyder A, Sala E. A novel representation of inter-site tumor heterogeneity from pre-treatment computed tomography textures classifies ovarian cancers by clinical outcome. Eur Radiol 2017;27(9):3991-4001.
  4. Gillies RJ, Kinahan PE, Hricak H. Radiomics: images are more than pictures, they are data. Radiology. 2016;278(2):563-77.
  5. Sala E, Mema E, Himoto Y, Veeraraghavan H, Brenton JD, Snyder A, Weigelt B, Vargas HA. Unraveling tumor heterogeneity using next generation imaging: radiomics, radiogenomics and habitat imaging. Clin Radiol 2016; 72 (1): 3-10.
  6. Sanduleanu S, Woodruff HC, de Jong EEC, van Timmeren JE, Jochems A, Dubois L, Lambin P. Tracking tumor biology with radiomics: A systematic review utilizing a radiomics quality score. Radiother Oncol. 2018 Jun;127(3):349-360.
  7. Shaikh F, Franc B, Sala E, Awan O, Hendrada K, Halabi S, Mohiuddin S, Malik S, Hadley D, Shrestha R. Translational radiomics – defining the strategy pipeline & considerations for application - part I: from methodology to clinical implementation. J Am Coll Radiol. 2018;15(3 Pt B):538-542.

Further Reading:
  • Adler, J., Lunz, S., Verdier, O., Schönlieb, C. B., & Öktem, O. (2018). Task adapted reconstruction for inverse problems. arXiv preprint arXiv:1809.00948.
  • Aviles-Rivero, A. I., Papadakis, N., Li, R., Sellars, P., Fan, Q., Tan, R. T., & Schönlieb, C. B. (2019, October). GraphX $$^\mathbf {\small NET}-$$ Chest X-Ray Classification Under Extreme Minimal Supervision. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 504-512). Springer, Cham.
  • Beer L, Sahin H, Bateman NW, Blazic I, Vargas HA, Veeraraghavan H, Kirby J, Fevrier-Sullivan B, Freymann JB, Jaffe C, Brenton JD, Miccó M, Nougaret S, Darcy KM, Maxwell LG, Conrads TP, Huang E, Sala E. Integration of proteomics with CT-based qualitative and texture features in high-grade serous ovarian cancer patients: An Exploratory Analysis. Eur Radiol, 2020; https://doi.org/10.1007/s00330-020-06755-3
  • Corona, V., Aviles-Rivero, A. I., Debroux, N., Graves, M., Le Guyader, C., Schönlieb, C. B., & Williams, G. (2019, June). Multi-tasking to Correct: Motion-Compensated MRI via Joint Reconstruction and Registration. In International Conference on Scale Space and Variational Methods in Computer Vision (pp. 263-274). Springer, Cham.
  • Jiménez-Sánchez A, Cybulska P, LaVigne K, Koplev S, Cast O, Couturier DL, Memon D, Selenica P, Nikolovski I, Mazaheri Y, Bykov Y, Geyer FC, Macintyre G, Gavarró LM, Drews RM, Gill MB, Papanastasiou AD, Sosa ER, Soslow RA, Walther T, Shen R, Chi DS, Park KJ, Hollmann T, Reis-Filho JS, Markowetz F, Beltrao P, Vargas HA, Zamarin D, Brenton JD, Snyder A, Weigelt B, Sala E, Miller M. Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy. Nat Genet, 2020; https://doi.org/10.1038/s41588-020-0630-5
  • Himoto Y, Veeraraghavan H, Zheng J, Zamarin D, Snyder A, Capanu M, Nougaret S, Vargas HA, Shitano F, Callahan M, Wang W, Sala E, Lakhman Y. Computed Tomography-Derived Radiomic Metrics Can Identify Responders To Immunotherapy In Ovarian Cancer. JCO PO 2019;3:1-13. 10.1200/PO.19.00038.
  • Liu, J., Aviles-Rivero, A. I., Ji, H., & Schönlieb, C. B. (2019). Rethinking medical image reconstruction via shape prior, going deeper and faster: Deep joint indirect registration and reconstruction. arXiv preprint arXiv:1912.07648.
  • Lunz, S., Öktem, O., & Schönlieb, C. B. (2018). Adversarial regularizers in inverse problems. In Advances in Neural Information Processing Systems (pp. 8507-8516).
  • Rundo L, Beer L, Ursprung S. Martin-Gonzalez P, Markowetz F, Brenton JD, Crispin-Ortuzar M, Sala E, Woitek R. Tissue-specific and interpretable sub-segmentation of whole tumour burden on CT images by unsupervised fuzzy clustering. Computers in Biology and Medicine, 2020; https://doi.org/10.1016/j.compbiomed.2020.103751
  • Ursprung S, Beer L, Bruining A, Woitek R, Stewart GD, Gallagher FA, Sala E. Radiomics of computed tomography and magnetic resonance imaging in renal cell carcinoma – a systematic review and meta-analysis. Eur Radiol, 2020 Feb 14. https://doi.org/10.1007/s00330-020-06666-3.