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Register a new userSuperpixels Based Marker Tracking Vs. Hue Thresholding In Rodent Biomechanics Application
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Added by
Omid Haji Maghsoudi
Publication date
2017
fields
Informatics Engineering
and research's language is
English
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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. We propose two methods to segment and track these markers: first, using SLIC superpixels segmentation with a tracker based on position, speed, shape, and color information of the segmented region in the previous frame; second, using a thresholding on hue channel following up with the same tracker. The comparison showed that the SLIC superpixels method was superior because the segmentation was more reliable and based on both color and spatial information.
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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 SLIC superpixel method. The 2D coordinates on the image plane are projected to a 3D domain using direct linear transform (DLT) 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. Finally, a probabilistic function is used to find the best match among superpixels. The method is evaluated for different difficulties for tracking of the markers and it achieves 95% correct labeling of markers.
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.
Augmented reality has the potential to improve operating room workflow by allowing physicians to see inside a patient through the projection of imaging directly onto the surgical field. For this to be useful the acquired imaging must be quickly and accurately registered with patient and the registration must be maintained. Here we describe a method for projecting a CT scan with Microsoft Hololens and then aligning that projection to a set of fiduciary markers. Radio-opaque stickers with unique QR-codes are placed on an object prior to acquiring a CT scan. The location of the markers in the CT scan are extracted and the CT scan is converted into a 3D surface object. The 3D object is then projected using the Hololens onto a table on which the same markers are placed. We designed an algorithm that aligns the markers on the 3D object with the markers on the table. To extract the markers and convert the CT into a 3D object took less than 5 seconds. To align three markers, it took $0.9 pm 0.2$ seconds to achieve an accuracy of $5 pm 2$ mm. These findings show that it is feasible to use a combined radio-opaque optical marker, placed on a patient prior to a CT scan, to subsequently align the acquired CT scan with the patient.
We consider the problem of segmenting an image into superpixels in the context of $k$-means clustering, in which we wish to decompose an image into local, homogeneous regions corresponding to the underlying objects. Our novel approach builds upon the widely used Simple Linear Iterative Clustering (SLIC), and incorporate a measure of objects structure based on the spectral residual of an image. Based on this combination, we propose a modified initialisation scheme and search metric, which helps keeps fine-details. This combination leads to better adherence to object boundaries, while preventing unnecessary segmentation of large, uniform areas, while remaining computationally tractable in comparison to other methods. We demonstrate through numerical and visual experiments that our approach outperforms the state-of-the-art techniques.
Visual multi-object tracking has the potential to accelerate many forms of quantitative analyses, especially in research communities investigating the motion, behavior, or social interactions within groups of animals. Despite its potential for increasing analysis throughput, complications related to accessibility, adaptability, accuracy, or scalable application arise with existing tracking systems. Several iterations of prototyping and testing have led us to a multi-object tracking system -- ABCTracker -- that is: accessible in both system as well as technical knowledge requirements, easily adaptable to new videos, and capable of producing accurate tracking data through a mixture of automatic and semi-automatic tracking features.
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