Abstract
The creation of 3D complete models of the woman breast that aggregate radiological and surface information is a crucial step for the development of surgery planning tools in the context of breast cancer. This requires the registration of interior and surface data of the breast, which has to recover large breast deformations caused by the different poses of the patient during data acquisition and has to deal with the lack of landmarks between both modalities, apart from the nipple. In this paper, the registration of Magnetic Resonance Imaging exams and 3D surface data reconstructed from Kinect (TM) acquisitions is explored using a biomechanical modelling of breast pose transformations combined with a free form deformation to finely match the data. The results are promising, with an average euclidean distance between the matched data of 0.81 +/- 0.09 mm being achieved.

Abstract
The small amount of public available medical images hinders the use of deep learning techniques for mammogram automatic diagnosis. Deep learning methods require large annotated training sets to be effective, however medical datasets are costly to obtain and suffer from large variability. In this work, a lightweight deep learning pipeline to detect, segment and classify anomalies in mammogram images is presented. First, data augmentation using the ground-truth annotation is performed and used by a cascade segmentation and classification methods. Results are obtained using the INbreast public database in the context of lesion detection and BI-RADS classification. Moreover, a pre-trained Convolutional Neural Network using ResNet50 is modified to generate the lesion regions proposals followed by a false positive reduction and contour refinement stages while a pre-trained VGG16 network is fine-tuned to classify mammograms. The detection and segmentation stage results show that the cascade configuration achieves a DICE of 0.83 without massive training while the multi-class classification exhibits an MAE of 0.58 with data augmentation.

Abstract
Particle tracking applied to video passive microrheology is conventionally done through methods that are far from being automatic. Creating mechanisms that decode the image set properties and correctly detect the tracer beads, to find their trajectories, is fundamental to facilitate microrheology studies. In this work, the adequacy of two particle detection methods - a Radial Symmetry-based approach and Gaussian fitting - for microrheology setups is tested, both on a synthetic database and on real data. Results show that it is possible to automate the particle tracking process in this scope, while ensuring high detection accuracy and sub-pixel precision, crucial for an adequate characterization of microrheology studies. © 2019, Springer Nature Switzerland AG.

Abstract
The deep inferior epigastric artery perforator (DIEAP) flap is the most common free flap used for breast reconstruction after a mastectomy. It makes use of the skin and fat of the lower abdomen to build a new breast mound either at the same time of the mastectomy or in a second surgery. This operation requires preoperative imaging studies to evaluate the branches - the perforators - that irrigate the tissue that will be used to reconstruct the breast mound. These branches will support tissue viability after the microsurgical ligation of the inferior epigastric vessels to the receptor vessels in the thorax. Usually through a computed tomography angiography (CTA), each perforator is manually identified and characterized by the imaging team, who will subsequently draw a map for the identification of the best vascular support for the reconstruction. In the current work we propose a semi-automatic methodology that aims at reducing the time and subjectivity inherent to the manual annotation. In 21 CTAs from patients proposed for breast reconstruction with DIEAP flaps, the subcutaneous region of each perforator was extracted, by means of a tracking procedure, whereas the intramuscular portion was detected through a minimum cost approach. Both were subsequently compared with the radiologist manual annotation. Results showed that the semi-automatic procedure was able to correctly detect the course of the DIEAPs with a minimum error (average error of 0.64 and 0.50 mm regarding the extraction of subcutaneous and intramuscular paths, respectively), taking little time to do so. The objective methodology is a promising tool in the automatic detection of perforators in CTA and can contribute to spare human resources and reduce subjectivity in the aforementioned task.

Abstract
Three-dimensional imaging techniques have been endeavouring at reaching affordable ubiquity. Nevertheless, its use in clinical practice can be hampered by less than naturally looking surfaces that greatly impact its visual inspection. This work considers the task of surface reconstruction from point clouds of non-rigid scenes acquired through structured-light-based methods, wherein the reconstructed surface contains some level of imperfection to be inpainted before visualized by experts in a clinically oriented context. Appertain to the topic, the recovery of colour information for missing or damaged partial regions is considered. A local geometry-based interpolation method is proposed for the reconstruction of the bare human torso and compared against a reference differential equations based inpainting method. Widely used perceptual distance-based metrics, such as PSNR, SSIM and MS-SSIM, and the evaluation from a panel of experienced breast cancer surgeons is presented for the discussion on inpainting quality assessment.

Abstract
The segmentation of blood vessels in medical images has been heavily studied, given its impact in several clinical practices. Deep Learning methods have been applied to supervised segmentation of blood vessels, mainly the retinal ones due to the availability of manual annotations. Despite their success, they typically minimize the Binary Cross Entropy loss, which does not penalize topological mistakes. These errors are relevant in graph-like structures such as blood vessel trees, as a missing segment or an inadequate merging or splitting of branches, may severely change the topology of the network and put at risk the extraction of vessel pathways and their characterization. In this paper, we propose an end-to-end network design comprising a cascade of a typical segmentation network and a Variational Auto-Encoder which, by learning a rich but compact latent space, is able to correct many topological incoherences. Our experiments in three of the most commonly used retinal databases, DRIVE, STARE, and CHASEDB1, show that the proposed model effectively learns representations inducing better segmentations in terms of topology, without hurting the usual pixel-wise metrics.