3D Hermite Transform Optical Flow Estimation in Left Ventricle CT Sequences

Heart diseases are the most important causes of death in the world and over the years, the study of cardiac movement has been carried out mainly in two dimensions, however, it is important to consider that the deformations due to the movement of the heart occur in a three-dimensional space. The 3 D + t analysis allows to describe most of the motions of the heart, for example, the twisting motion that takes place on every beat cycle that allows us identifying abnormalities of the heart walls. Therefore, it is necessary to develop algorithms that help specialists understand the cardiac movement. In this work, we developed a new approach to determine the cardiac movement in three dimensions using a differential optical flow approach in which we use the steered Hermite transform (SHT) which allows us to decompose cardiac volumes taking advantage of it as a model of the human vision system (HVS). Our proposal was tested in complete cardiac computed tomography (CT) volumes ( 3 D + t ), as well as its respective left ventricular segmentation. The robustness to noise was tested with good results. The evaluation of the results was carried out through errors in forwarding reconstruction, from the volume at time t to time t + 1 using the optical flow obtained (interpolation errors). The parameters were tuned extensively. In the case of the 2D algorithm, the interpolation errors and normalized interpolation errors are very close and below the values reported in ground truth flows. In the case of the 3D algorithm, the results were compared with another similar method in 3D and the interpolation errors remained below 0.1. These results of interpolation errors for complete cardiac volumes and the left ventricle are shown graphically for clarity. Finally, a series of graphs are observed where the characteristic of contraction and dilation of the left ventricle is evident through the representation of the 3D optical flow

Deformable Models for Segmentation Based on Local Analysis

Segmentation tasks in medical imaging represent an exhaustive challenge for scientists since the image acquisition nature yields issues that hamper the correct reconstruction and visualization processes. Depending on the specific image modality, we have to consider limitations such as the presence of noise, vanished edges, or high intensity differences, known, in most cases, as inhomogeneities. New algorithms in segmentation are required to provide a better performance. This paper presents a new unified approach to improve traditional segmentation methods as Active Shape Models and Chan-Vese model based on level set. The approach introduces a combination of local analysis implementations with classic segmentation algorithms that incorporates local texture information given by the Hermite transform and Local Binary Patterns. The mixture of both region-based methods and local descriptors highlights relevant regions by considering extra information which is helpful to delimit structures. We performed segmentation experiments on 2D images including midbrain in Magnetic Resonance Imaging and heart’s left ventricle endocardium in Computed Tomography. Quantitative evaluation was obtained with Dice coefficient and Hausdorff distance measures. Results display a substantial advantage over the original methods when we include our characterization schemes. We propose further research validation on different organ structures with promising results

Robust cardiac segmentation corrected with heuristics.

Cardiovascular diseases related to the right side of the heart, such as Pulmonary Hypertension, are some of the leading causes of death among the Mexican (and worldwide) population. To avoid invasive techniques such as catheterizing the heart, improving the segmenting performance of medical echocardiographic systems can be an option to early detect diseases related to the right-side of the heart. While current medical imaging systems perform well segmenting automatically the left side of the heart, they typically struggle segmenting the right-side cavities. This paper presents a robust cardiac segmentation algorithm based on the popular U-NET architecture capable of accurately segmenting the four cavities with a reduced training dataset. Moreover, we propose two additional steps to improve the quality of the results in our machine learning model, 1) a segmentation algorithm capable of accurately detecting cone shapes (as it has been trained and refined with multiple data sources) and 2) a post-processing step which refines the shape and contours of the segmentation based on heuristics provided by the clinicians. Our results demonstrate that the proposed techniques achieve segmentation accuracy comparable to state-of-the-art methods in datasets commonly used for this practice, as well as in datasets compiled by our medical team. Furthermore, we tested the validity of the post-processing correction step within the same sequence of images and demonstrated its consistency with manual segmentations performed by clinicians

Sargassum detection and path estimation using neural networks

Sargassum has affected the Mexican Caribbean coasts since 2015 in atypical amounts, causing economic and ecological problems. Removal once it reaches the coast is complex since it is not easily separated from the sand, damaging dune vegetation, heavy transport compacts the sand and further deteriorates the coastline. Therefore, it is important to detect and estimate the sargassum mats path to optimize the collection efforts in the water. There have been some improvements in systems that rely on satellite images to determine areas and possible paths of sargassum, but these methods do not solve the problems near the coastline where the big mats observed in deep sea end up segregating in little mats which often do not show up in the satellite images. Besides, the temporal scales of nearshore sargassum dynamics are characterized by finer temporal resolution. This paper focuses on cameras located near the coast of Puerto Morelos reef lagoon where images are recorded of both beach and near-coastal sea. First, we apply preprocessing techniques based on time that allows us to discriminate the moving sargassum mats from the static sea bottom, then, using classic image processing techniques and neural networks we detect, trace, and estimate the path of the mat towards the place of arrival on the beach. We compared classic algorithms with neural networks. Some of the algorithms we tested are k-means and random forest for segmentation and dense optical flow to follow and estimate the path. This new methodology allows to supervise in real time the demeanor of sargassum close to shore without complex technical support

Sargassum detection and path estimation using neural networks

Sargassum has affected the Mexican Caribbean coasts since 2015 in atypical amounts, causing economic and ecological problems. Removal once it reaches the coast is complex since it is not easily separated from the sand, damaging dune vegetation, heavy transport compacts the sand and further deteriorates the coastline. Therefore, it is important to detect and estimate the sargassum mats path to optimize the collection efforts in the water. There have been some improvements in systems that rely on satellite images to determine areas and possible paths of sargassum, but these methods do not solve the problems near the coastline where the big mats observed in deep sea end up segregating in little mats which often do not show up in the satellite images. Besides, the temporal scales of nearshore sargassum dynamics are characterized by finer temporal resolution. This paper focuses on cameras located near the coast of Puerto Morelos reef lagoon where images are recorded of both beach and near-coastal sea. First, we apply preprocessing techniques based on time that allows us to discriminate the moving sargassum mats from the static sea bottom, then, using classic image processing techniques and neural networks we detect, trace, and estimate the path of the mat towards the place of arrival on the beach. We compared classic algorithms with neural networks. Some of the algorithms we tested are k-means and random forest for segmentation and dense optical flow to follow and estimate the path. This new methodology allows to supervise in real time the demeanor of sargassum close to shore without complex technical support.Environmental Fluid Mechanic

Feature-based 3D+t descriptors of hyperactivated human sperm beat patterns

The flagellar movement of the mammalian sperm plays a crucial role in fertilization. In the female reproductive tract, human spermatozoa undergo a process called capacitation which promotes changes in their motility. Only capacitated spermatozoa may be hyperactivated and only those that transition to hyperactivated motility are capable of fertilizing the egg. Hyperactivated motility is characterized by asymmetric flagellar bends of greater amplitude and lower frequency. Historically, clinical fertilization studies have used two-dimensional analysis to classify sperm motility, despite the inherently three-dimensional (3D) nature of sperm motion. Recent research has described several 3D beating features of sperm flagella. However, the 3D motility pattern of hyperactivated spermatozoa has not yet been characterized. One of the main challenges in classifying these patterns in 3D is the lack of a ground-truth reference, as it can be difficult to visually assess differences in flagellar beat patterns. Additionally, it is worth noting that only a relatively small proportion, approximately 10-20% of sperm incubated under capacitating conditions exhibit hyperactivated motility. In this work, we used a multifocal image acquisition system that can acquire, segment, and track sperm flagella in 3D+t. We developed a feature-based vector that describes the spatio-temporal flagellar sperm motility patterns by an envelope of ellipses. The classification results obtained using our 3D feature-based descriptors can serve as potential label for future work involving deep neural networks. By using the classification results as labels, it will be possible to train a deep neural network to automatically classify spermatozoa based on their 3D flagellar beating patterns. We demonstrated the effectiveness of the descriptors by applying them to a dataset of human sperm cells and showing that they can accurately differentiate between non-hyperactivated and hyperactivated 3D motility patterns of the sperm cells. This work contributes to the understanding of 3D flagellar hyperactive motility patterns and provides a framework for research in the fields of human and animal fertility