Background and Objective: Surgical robotics tends to develop cognitive control architectures to provide certain degree of autonomy to improve patient safety and surgery outcomes, while decreasing the required surgeons' cognitive load dedicated to low level decisions. Cognition needs workspace perception, which is an essential step towards automatic decision-making and task planning capabilities. Robust and accurate detection and tracking in minimally invasive surgery suffers from limited visibility, occlusions, anatomy deformations and camera movements., Method: This paper develops a robust methodology to detect and track anatomical structures in real time to be used in automatic control of robotic systems and augmented reality. The work focuses on the experimental validation in highly challenging surgery: fetoscopic repair of Open Spina Bifida. The proposed method is based on two sequential steps: first, selection of relevant points (contour) using a Convolutional Neural Network and, second, reconstruction of the anatomical shape by means of deformable geometric primitives., Results: The methodology performance was validated with different scenarios. Synthetic scenario tests, designed for extreme validation conditions, demonstrate the safety margin offered by the methodology with respect to the nominal conditions during surgery. Real scenario experiments have demonstrated the validity of the method in terms of accuracy, robustness and computational efficiency., Conclusions: This paper presents a robust anatomical structure detection in present of abrupt camera movements, severe occlusions and deformations. Even though the paper focuses on a case study, Open Spina Bifida, the methodology is applicable in all anatomies which contours can be approximated by geometric primitives. The methodology is designed to provide effective inputs to cognitive robotic control and augmented reality systems that require accurate tracking of sensitive anatomies., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Narcis Sayols reports financial support was provided by Cellex Foundation. Albert Hernansanz reports financial support was provided by Cellex Foundation. Johanna Parra reports financial support was provided by Cellex Foundation. Elisenda Eixarch reports financial support was provided by Cellex Foundation. Eduard Gratacos reports financial support was provided by Cellex Foundation. Alicia Casals reports financial support was provided by Cellex Foundation. Elisenda Eixarch reports financial support was provided by Departament de Salut de la Generalitat de Catalunya., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)