Classification of Primary versus Metastatic Pancreatic Tumor Cells Using Multiple Biomarkers and Whole Slide Imaging

Pancreatic cancer is a challenging cancer with a high mortality rate and a 5-year survival rate between 2% to 9%. The role of biomarkers is crucial in cancer prognosis, diagnosis, and predicting the possible responses to a specific therapy. The Discovery and development of various types of biomarkers have been studied intensively in the hope of determining the best treatment approaches, better management, and possibly cure of this deadly cancer. However, metastasis, responsible for about 90% of the deaths from cancer, is still poorly understood. A few research that have investigated the expression of a particular biomarker or a panel of biomarkers in the primary and secondary (metastatic) tumor demonstrates that the expression of different biomarkers in the primary and secondary tumor sites is not necessarily the same, even though the primary and metastatic tumor cells are originated from the same organ. In this project, we aim to design a classifier to distinguish between primary and secondary tumor cells based on their uptake of different biomarkers, using immunofluorescence whole slide imaging. For this purpose, we first register consecutive images of the same slide together to be able to locate multiple biomarkers that belong to a cell and later we design our classifier based on vectors that show the presence or absence of multiple antibodies in addition to the amount of that antibody in a tumor cell. Advisor: Khalid Sayoo

Registration of serial sections: An evaluation method based on distortions of the ground truths

Registration of histological serial sections is a challenging task. Serial sections exhibit distortions and damage from sectioning. Missing information on how the tissue looked before cutting makes a realistic validation of 2D registrations extremely difficult. This work proposes methods for ground-truth-based evaluation of registrations. Firstly, we present a methodology to generate test data for registrations. We distort an innately registered image stack in the manner similar to the cutting distortion of serial sections. Test cases are generated from existing 3D data sets, thus the ground truth is known. Secondly, our test case generation premises evaluation of the registrations with known ground truths. Our methodology for such an evaluation technique distinguishes this work from other approaches. Both under- and over-registration become evident in our evaluations. We also survey existing validation efforts. We present a full-series evaluation across six different registration methods applied to our distorted 3D data sets of animal lungs. Our distorted and ground truth data sets are made publicly available.Comment: Supplemental data available under https://zenodo.org/record/428244

Libro de actas. XXXV Congreso Anual de la Sociedad Española de Ingeniería Biomédica

596 p.CASEIB2017 vuelve a ser el foro de referencia a nivel nacional para el intercambio científico de conocimiento, experiencias y promoción de la I D i en Ingeniería Biomédica. Un punto de encuentro de científicos, profesionales de la industria, ingenieros biomédicos y profesionales clínicos interesados en las últimas novedades en investigación, educación y aplicación industrial y clínica de la ingeniería biomédica. En la presente edición, más de 160 trabajos de alto nivel científico serán presentados en áreas relevantes de la ingeniería biomédica, tales como: procesado de señal e imagen, instrumentación biomédica, telemedicina, modelado de sistemas biomédicos, sistemas inteligentes y sensores, robótica, planificación y simulación quirúrgica, biofotónica y biomateriales. Cabe destacar las sesiones dedicadas a la competición por el Premio José María Ferrero Corral, y la sesión de competición de alumnos de Grado en Ingeniería biomédica, que persiguen fomentar la participación de jóvenes estudiantes e investigadores