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Medical Image Segmentation: How to integrate object appearance/shape models and interactive correction with minimum user intervention?

Grant number: 15/09446-7
Support type:Scholarships in Brazil - Post-Doctorate
Effective date (Start): November 01, 2015
Effective date (End): June 11, 2017
Field of knowledge:Physical Sciences and Mathematics - Computer Science - Computing Methodologies and Techniques
Principal Investigator:Alexandre Xavier Falcão
Grantee:Thiago Vallin Spina
Home Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Associated scholarship(s):16/11853-2 - SAMSAM: Segmentation for Analysis and Measurements in the Shoot Apical Meristem, BE.EP.PD


Problem: Medical image segmentation (in MRI and CT modalities) aims to delineate the human body's anatomical structures in a precise way to allow quantitative analysis in the diagnosis and treatment of diseases. Appearance/shape models of theses structures may be learned and applied to segment new images automatically. However, when automatic segmentation fails these methods rarely provide effective and efficient solutions to allow the interactive correction of segmentation errors without affecting parts already accepted as correct, and that minimize the user's involvement. In practice, manual/interactive segmentation is done from scratch quite often - a tedious task subject to user mistakes due to weariness and carelessness.Proposal: This postdoctoral research project aims to investigate solutions that integrate in an effective and efficiente way automatic medical image segmentation based on object appearance/shape models and interactive correction. In this context, the project aims to continue and integrate preliminary works in our group that: (a) convert \emph{any} initial segmentation into an optimum-path forest - an acyclic graph where every object of interest is represented by the union of trees rooted at nodes (seeds) inside them; (b) allow the differential correction of segmentation by the addition and removal of markers (connected seed sets) - i.e., the addition and removal of forest trees; and (c) correct minor flaws in segmentation through the smoothing of the object's boundaries. This proposal includes the development and validation of new solutions to item (a) and the validation of the current solutions to items (a) and (c). The interactive correction of automatic segmentation also allows the update of the object appearance/shape models through the inclusion of a new training sample. This aspect will also be assessed in this work.Justification and expected results: The project will be partially developed in Brazil and at the University of Sheffield, UK, under the supervision of Prof. Dr. Alejandro Frangi, thereby increasing the candidate's international experience and our group's international cooperation network. While abroad, the candidate will implement the developed methods in a public domain software (, further validating the methods in images annotated by experts to increase the impact of the work beyond the expected publications.