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

Deep Learning-Based Multiple Object Visual Tracking on Embedded System for IoT and Mobile Edge Computing Applications

Compute and memory demands of state-of-the-art deep learning methods are still a shortcoming that must be addressed to make them useful at IoT end-nodes. In particular, recent results depict a hopeful prospect for image processing using Convolutional Neural Netwoks, CNNs, but the gap between software and hardware implementations is already considerable for IoT and mobile edge computing applications due to their high power consumption. This proposal performs low-power and real time deep learning-based multiple object visual tracking implemented on an NVIDIA Jetson TX2 development kit. It includes a camera and wireless connection capability and it is battery powered for mobile and outdoor applications. A collection of representative sequences captured with the on-board camera, dETRUSC video dataset, is used to exemplify the performance of the proposed algorithm and to facilitate benchmarking. The results in terms of power consumption and frame rate demonstrate the feasibility of deep learning algorithms on embedded platforms although more effort to joint algorithm and hardware design of CNNs is needed.Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessibl

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

Structured Light-Based 3D Reconstruction System for Plants.

Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance

M2U-net: Effective and efficient retinal vessel segmentation for real-world applications

In this paper, we present a novel neural network architecture for retinal vessel segmentation that improves over the state of the art on two benchmark datasets, is the first to run in real time on high resolution images, and its small memory and processing requirements make it deployable in mobile and embedded systems. The M2U-Net has a new encoder-decoder architecture that is inspired by the U-Net. It adds pretrained components of MobileNetV2 in the encoder part and novel contractive bottleneck blocks in the decoder part that, combined with bilinear upsampling, drastically reduce the parameter count to 0.55M compared to 31.03M in the original U-Net. We have evaluated its performance against a wide body of previously published results on three public datasets. On two of them, the M2U-Net achieves new state-of-the-art performance by a considerable margin. When implemented on a GPU, our method is the first to achieve real-time inference speeds on high-resolution fundus images. We also implemented our proposed network on an ARM-based embedded system where it segments images in between 0.6 and 15 sec, depending on the resolution. Thus, the M2U-Net enables a number of applications of retinal vessel structure extraction, such as early diagnosis of eye diseases, retinal biometric authentication systems, and robot assisted microsurgery