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We consider the problem of finding an accurate representation of neuron shapes, extracting sub-cellular features, and classifying neurons based on neuron shapes. In neuroscience research, the skeleton representation is often used as a compact and abstract representation of neuron shapes. However, existing methods are limited to getting and analyzing “curve” skeletons which can only be applied for tubular shapes. This paper presents a 3D neuron morphology analysis method for more general and complex neuron shapes. First, we introduce the concept of skeleton mesh to represent general neuron shapes and propose a novel method for computing mesh representations from 3D surface point clouds. A skeleton graph is then obtained from skeleton mesh and is used to extract sub-cellular features. Finally, an unsupervised learning method is used to embed the skeleton graph for neuron classification. Extensive experiment results are provided and demonstrate the robustness of our method to analyze neuron morphology.

 

Abstract This paper presents a method for time-lapse 3D cell analysis. Specifically, we consider the problem of accurately localizing and quantitatively analyzing sub-cellular features, and for tracking individual cells from time-lapse 3D confocal cell image stacks. The heterogeneity of cells and the volume of multi-dimensional images presents a major challenge for fully automated analysis of morphogenesis and development of cells. This paper is motivated by the pavement cell growth process, and building a quantitative morphogenesis model. We propose a deep feature based segmentation method to accurately detect and label each cell region. An adjacency graph based method is used to extract sub-cellular features of the segmented cells. Finally, the robust graph based tracking algorithm using multiple cell features is proposed for associating cells at different time instances. We also demonstrate the generality of our tracking method on C. elegans fluorescent nuclei imagery. Extensive experiment results are provided and demonstrate the robustness of the proposed method. The code is available on and the method is available as a service through the BisQue portal. 

Each year, underwater remotely operated vehicles (ROVs) collect thousands of hours of video of unexplored ocean habitats revealing a plethora of information regarding biodiversity on Earth. However, fully utilizing this information remains a challenge as proper annotations and analysis require trained scientists’ time, which is both limited and costly. To this end, we present a Dataset for Underwater Substrate and Invertebrate Analysis (DUSIA), a benchmark suite and growing large-scale dataset to train, validate, and test methods for temporally localizing four underwater substrates as well as temporally and spatially localizing 59 underwater invertebrate species. DUSIA currently includes over ten hours of footage across 25 videos captured in 1080p at 30 fps by an ROV following pre-planned transects across the ocean floor near the Channel Islands of California. Each video includes annotations indicating the start and end times of substrates across the video in addition to counts of species of interest. Some frames are annotated with precise bounding box locations for invertebrate species of interest, as seen in Fig. 1. To our knowledge, DUSIA is the first dataset of its kind for deep sea exploration, with video from a moving camera, that includes substrate annotations and invertebrate species that are present at significant depths where sunlight does not penetrate. Additionally, we present the novel context-driven object detector (CDD) where we use explicit substrate classification to influence an object detection network to simultaneously predict a substrate and species class influenced by that substrate. We also present a method for improving training on partially annotated bounding box frames. Finally, we offer a baseline method for automating the counting of invertebrate species of interest.

 

In computer vision, single-image super-resolution (SISR) has been extensively explored using convolutional neural networks (CNNs) on optical images, but images outside this domain, such as those from scientific experiments, are not well investigated. Experimental data is often gathered using non-optical methods, which alters the metrics for image quality. One such example is electron backscatter diffraction (EBSD), a materials characterization technique that maps crystal arrangement in solid materials, which provides insight into processing, structure, and property relationships. We present a broadly adaptable approach for applying state-of-art SISR networks to generate super-resolved EBSD orientation maps. This approach includes quaternion-based orientation recognition, loss functions that consider rotational effects and crystallographic symmetry, and an inference pipeline to convert network output into established visualization formats for EBSD maps. The ability to generate physically accurate, high-resolution EBSD maps with super-resolution enables high-throughput characterization and broadens the capture capabilities for three-dimensional experimental EBSD datasets.

 

Abstract This paper presents a deep-learning-based workflow to detect synapses and predict their neurotransmitter type in the primitive chordate Ciona intestinalis ( Ciona ) electron microscopic (EM) images. Identifying synapses from EM images to build a full map of connections between neurons is a labor-intensive process and requires significant domain expertise. Automation of synapse classification would hasten the generation and analysis of connectomes. Furthermore, inferences concerning neuron type and function from synapse features are in many cases difficult to make. Finding the connection between synapse structure and function is an important step in fully understanding a connectome. Class Activation Maps derived from the convolutional neural network provide insights on important features of synapses based on cell type and function. The main contribution of this work is in the differentiation of synapses by neurotransmitter type through the structural information in their EM images. This enables the prediction of neurotransmitter types for neurons in Ciona , which were previously unknown. The prediction model with code is available on GitHub. 

Objective and Impact Statement . We propose an automated method of predicting Normal Pressure Hydrocephalus (NPH) from CT scans. A deep convolutional network segments regions of interest from the scans. These regions are then combined with MRI information to predict NPH. To our knowledge, this is the first method which automatically predicts NPH from CT scans and incorporates diffusion tractography information for prediction. Introduction . Due to their low cost and high versatility, CT scans are often used in NPH diagnosis. No well-defined and effective protocol currently exists for analysis of CT scans for NPH. Evans’ index, an approximation of the ventricle to brain volume using one 2D image slice, has been proposed but is not robust. The proposed approach is an effective way to quantify regions of interest and offers a computational method for predicting NPH. Methods . We propose a novel method to predict NPH by combining regions of interest segmented from CT scans with connectome data to compute features which capture the impact of enlarged ventricles by excluding fiber tracts passing through these regions. The segmentation and network features are used to train a model for NPH prediction. Results . Our method outperforms the current state-of-the-art by 9 precision points and 29 recall points. Our segmentation model outperforms the current state-of-the-art in segmenting the ventricle, gray-white matter, and subarachnoid space in CT scans. Conclusion . Our experimental results demonstrate that fast and accurate volumetric segmentation of CT brain scans can help improve the NPH diagnosis process, and network properties can increase NPH prediction accuracy.