Omid Haji Maghsoudi

Three-dimensional radiomic analysis of digital breast tomosynthesis outperformed two-dimensional measures in breast cancer risk assessment.

Studying animal locomotion improves our understanding of motor control and aids in the treatment of motor impairment. Mice are a premier model of human disease and are the model system of choice for much of basic neuroscience. Placement of the tips of appendages, here paws, is typically critical for locomotion. Tracking paws from a video is difficult, however, due to frequent occlusions and collisions. We propose a method and provide software to track the paws of rodents. We use a superpixel-based method to segment the paws, direct linear transform to perform 3D reconstruction, a 3D Kalman filter (KF) to solve the matching problem and label paws across frames, and spline fits through time to resolve common collisions. The automated method was compared to manual tracking. The method had an average of 2.54 mistakes requiring manual correction per 1000 frames with a maximum of 5.29 possible errors while these values were estimates of the expected errors. We present an algorithm and its implementation to track the paws of running rodents. This algorithm can be applied to different animals as long as the tips of the legs can be differentiated from the background and other parts of the body using color features. The presented algorithm provides a robust tool for future studies in multiple fields, where precise quantification of locomotor behavior from a high-speed video is required. We further present a graphical user interface (GUI) to track, visualize, and edit the tracking data.

Examining locomotion has improved our basic understanding of motor control and aided in treating motor impairment. Mice and rats are premier models of human disease and increasingly the model systems of choice for basic neuroscience. High frame rates (250 Hz) are needed to quantify the kinematics of these running rodents. Manual tracking, especially for multiple markers, becomes time‐consuming and impossible for large sample sizes. Therefore, the need for automatic segmentation of these markers has grown in recent years. Here, we address this need by presenting a method to segment the markers using the simple linear iterative clustering superpixel method. The two‐dimensional coordinates on the image plane are projected to a three‐dimensional (3D) domain using direct linear transform and a 3D Kalman filter has been used to predict the position of markers based on the speed and position of markers from the previous frames. A probabilistic function is used to find the best match from among superpixels. The method is evaluated for different difficulties for tracking of the markers, and it achieves 95% correct labeling of markers. Finally, the method was used to analyze data from an ongoing study seeking to improve recovery from spinal cord injury in rats

Examining locomotion has improved our basic understanding of motor control and aided in treating motor impairment. Mice and rats are the model system of choice for basic neuroscience studies of human...

Examining locomotion has improved our basic understanding of motor control and aided in treating motor impairment. Mice and rats are the model system of choice for basic neuroscience studies of human disease. High frame rates are needed to quantify the kinematics of running rodents, due to their high stride frequency. Manual tracking, especially for multiple body landmarks, becomes extremely time-consuming. To overcome these limitations, we proposed the use of superpixels based image segmentation as superpixels utilized both spatial and color information for segmentation. We segmented some parts of body and tested the success of segmentation as a function of color space and SLIC segment size. We used a simple merging function to connect the segmented regions considered as neighbor and having the same intensity value range. In addition, 28 features were extracted, and t-SNE was used to demonstrate how much the methods are capable to differentiate the regions. Finally, we compared the segmented regions to a manually outlined region. The results showed for segmentation, using the RGB image was slightly better compared to the hue channel. For merg- ing and classification, however, the hue representation was better as it captures the relevant color information in a single channel.

Studying animal locomotion improves our understanding of motor control and aids in the treatment of motor impairment. Mice are a premier model of human disease and are the model system of choice for much of basic neuroscience. High frame rates (250 Hz) are needed to quantify the kinematics of these running rodents. Manual tracking, especially for multiple markers, becomes time-consuming and impossible. Therefore, an automated method is necessary. We propose a method to track the paws of the animal in the following manner: first, segmenting all the possible paws based on color; second, classifying the segmented objects using a support vector machine (SVM) and neural network (NN); third, classifying the objects using the kinematic features of the running animal, coupled with texture features from earlier frames; and finally, detecting and handling collisions to assure the correctness of labelled paws. The proposed method is validated in sixty 1,000 frame video sequences (4 seconds) captured by four cameras from five mice. The total sensitivity for tracking of the front and hind paw is 99.70% using the SVM classifier and 99.76% using the NN classifier. In addition, we show the feasibility of 3D reconstruction using the four camera system.