Three-Dimensional GPU-Accelerated Active Contours for Automated Localization of Cells in Large Images

Cell segmentation in microscopy is a challenging problem, since cells are often asymmetric and densely packed. This becomes particularly challenging for extremely large images, since manual intervention and processing time can make segmentation intractable. In this paper, we present an efficient and highly parallel formulation for symmetric three-dimensional (3D) contour evolution that extends previous work on fast two-dimensional active contours. We provide a formulation for optimization on 3D images, as well as a strategy for accelerating computation on consumer graphics hardware. The proposed software takes advantage of Monte-Carlo sampling schemes in order to speed up convergence and reduce thread divergence. Experimental results show that this method provides superior performance for large 2D and 3D cell segmentation tasks when compared to existing methods on large 3D brain images

DPP-PMRF: Rethinking Optimization for a Probabilistic Graphical Model Using Data-Parallel Primitives

We present a new parallel algorithm for probabilistic graphical model optimization. The algorithm relies on data-parallel primitives (DPPs), which provide portable performance over hardware architecture. We evaluate results on CPUs and GPUs for an image segmentation problem. Compared to a serial baseline, we observe runtime speedups of up to 13X (CPU) and 44X (GPU). We also compare our performance to a reference, OpenMP-based algorithm, and find speedups of up to 7X (CPU).Comment: LDAV 2018, October 201

Real-Time analysis and visualization for single-molecule based super-resolution microscopy

Accurate multidimensional localization of isolated fluorescent emitters is a time consuming process in single-molecule based super-resolution microscopy. We demonstrate a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. Compatible with high frame rates of EM-CCD cameras, it relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation. A combination with Gaussian fitting allows direct access to 3D localization. Automatic feedback control ensures optimal molecule density throughout the acquisition process. With this method, we significantly improve the efficiency and feasibility of localization-based super-resolution microscopy

Decreasing time consumption of microscopy image segmentation through parallel processing on the GPU

The computational performance of graphical processing units (GPUs) has improved significantly. Achieving speedup factors of more than 50x compared to single-threaded CPU execution are not uncommon due to parallel processing. This makes their use for high throughput microscopy image analysis very appealing. Unfortunately, GPU programming is not straightforward and requires a lot of programming skills and effort. Additionally, the attainable speedup factor is hard to predict, since it depends on the type of algorithm, input data and the way in which the algorithm is implemented. In this paper, we identify the characteristic algorithm and data-dependent properties that significantly relate to the achievable GPU speedup. We find that the overall GPU speedup depends on three major factors: (1) the coarse-grained parallelism of the algorithm, (2) the size of the data and (3) the computation/memory transfer ratio. This is illustrated on two types of well-known segmentation methods that are extensively used in microscopy image analysis: SLIC superpixels and high-level geometric active contours. In particular, we find that our used geometric active contour segmentation algorithm is very suitable for parallel processing, resulting in acceleration factors of 50x for 0.1 megapixel images and 100x for 10 megapixel images

Layered Interpretation of Street View Images

We propose a layered street view model to encode both depth and semantic information on street view images for autonomous driving. Recently, stixels, stix-mantics, and tiered scene labeling methods have been proposed to model street view images. We propose a 4-layer street view model, a compact representation over the recently proposed stix-mantics model. Our layers encode semantic classes like ground, pedestrians, vehicles, buildings, and sky in addition to the depths. The only input to our algorithm is a pair of stereo images. We use a deep neural network to extract the appearance features for semantic classes. We use a simple and an efficient inference algorithm to jointly estimate both semantic classes and layered depth values. Our method outperforms other competing approaches in Daimler urban scene segmentation dataset. Our algorithm is massively parallelizable, allowing a GPU implementation with a processing speed about 9 fps.Comment: The paper will be presented in the 2015 Robotics: Science and Systems Conference (RSS

DEEP FULLY RESIDUAL CONVOLUTIONAL NEURAL NETWORK FOR SEMANTIC IMAGE SEGMENTATION

Department of Computer Science and EngineeringThe goal of semantic image segmentation is to partition the pixels of an image into semantically meaningful parts and classifying those parts according to a predefined label set. Although object recognition models achieved remarkable performance recently and they even surpass human???s ability to recognize objects, but semantic segmentation models are still behind. One of the reason that makes semantic segmentation relatively a hard problem is the image understanding at pixel level by considering global context as oppose to object recognition. One other challenge is transferring the knowledge of an object recognition model for the task of semantic segmentation. In this thesis, we are delineating some of the main challenges we faced approaching semantic image segmentation with machine learning algorithms. Our main focus was how we can use deep learning algorithms for this task since they require the least amount of feature engineering and also it was shown that such models can be applied to large scale datasets and exhibit remarkable performance. More precisely, we worked on a variation of convolutional neural networks (CNN) suitable for the semantic segmentation task. We proposed a model called deep fully residual convolutional networks (DFRCN) to tackle this problem. Utilizing residual learning makes training of deep models feasible which ultimately leads to having a rich powerful visual representation. Our model also benefits from skip-connections which ease the propagation of information from the encoder module to the decoder module. This would enable our model to have less parameters in the decoder module while it also achieves better performance. We also benchmarked the effective variation of the proposed model on a semantic segmentation benchmark. We first make a thorough review of current high-performance models and the problems one might face when trying to replicate such models which mainly arose from the lack of sufficient provided information. Then, we describe our own novel method which we called deep fully residual convolutional network (DFRCN). We showed that our method exhibits state of the art performance on a challenging benchmark for aerial image segmentation.clos

Combinatorial Continuous Maximal Flows

Maximum flow (and minimum cut) algorithms have had a strong impact on computer vision. In particular, graph cuts algorithms provide a mechanism for the discrete optimization of an energy functional which has been used in a variety of applications such as image segmentation, stereo, image stitching and texture synthesis. Algorithms based on the classical formulation of max-flow defined on a graph are known to exhibit metrication artefacts in the solution. Therefore, a recent trend has been to instead employ a spatially continuous maximum flow (or the dual min-cut problem) in these same applications to produce solutions with no metrication errors. However, known fast continuous max-flow algorithms have no stopping criteria or have not been proved to converge. In this work, we revisit the continuous max-flow problem and show that the analogous discrete formulation is different from the classical max-flow problem. We then apply an appropriate combinatorial optimization technique to this combinatorial continuous max-flow CCMF problem to find a null-divergence solution that exhibits no metrication artefacts and may be solved exactly by a fast, efficient algorithm with provable convergence. Finally, by exhibiting the dual problem of our CCMF formulation, we clarify the fact, already proved by Nozawa in the continuous setting, that the max-flow and the total variation problems are not always equivalent.Comment: 26 page