Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks. Conclusions: By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. There is a pressing need for visualization and analysis tools for 5-D live cell image data. We combine accurate unsupervised processes with an intuitive visualization of the results. Our validation interface allows for each data set to be corrected to 100% accuracy, ensuring that downstream data analysis is accurate and verifiable. Our tool is the first to combine all of these aspects, leveraging the synergies obtained by utilizing validation information from stereo visualization to improve the low level image processing tasks.Comment: BioVis 2014 conferenc

Assessing hyper parameter optimization and speedup for convolutional neural networks

The increased processing power of graphical processing units (GPUs) and the availability of large image datasets has fostered a renewed interest in extracting semantic information from images. Promising results for complex image categorization problems have been achieved using deep learning, with neural networks comprised of many layers. Convolutional neural networks (CNN) are one such architecture which provides more opportunities for image classification. Advances in CNN enable the development of training models using large labelled image datasets, but the hyper parameters need to be specified, which is challenging and complex due to the large number of parameters. A substantial amount of computational power and processing time is required to determine the optimal hyper parameters to define a model yielding good results. This article provides a survey of the hyper parameter search and optimization methods for CNN architectures

Automatic Parameter Adaptation for Multi-object Tracking

Object tracking quality usually depends on video context (e.g. object occlusion level, object density). In order to decrease this dependency, this paper presents a learning approach to adapt the tracker parameters to the context variations. In an offline phase, satisfactory tracking parameters are learned for video context clusters. In the online control phase, once a context change is detected, the tracking parameters are tuned using the learned values. The experimental results show that the proposed approach outperforms the recent trackers in state of the art. This paper brings two contributions: (1) a classification method of video sequences to learn offline tracking parameters, (2) a new method to tune online tracking parameters using tracking context.Comment: International Conference on Computer Vision Systems (ICVS) (2013

A Comparison of Nature Inspired Algorithms for Multi-threshold Image Segmentation

In the field of image analysis, segmentation is one of the most important preprocessing steps. One way to achieve segmentation is by mean of threshold selection, where each pixel that belongs to a determined class islabeled according to the selected threshold, giving as a result pixel groups that share visual characteristics in the image. Several methods have been proposed in order to solve threshold selectionproblems; in this work, it is used the method based on the mixture of Gaussian functions to approximate the 1D histogram of a gray level image and whose parameters are calculated using three nature inspired algorithms (Particle Swarm Optimization, Artificial Bee Colony Optimization and Differential Evolution). Each Gaussian function approximates thehistogram, representing a pixel class and therefore a threshold point. Experimental results are shown, comparing in quantitative and qualitative fashion as well as the main advantages and drawbacks of each algorithm, applied to multi-threshold problem.Comment: 16 pages, this is a draft of the final version of the article sent to the Journa

BSUV-Net: a fully-convolutional neural network for background subtraction of unseen videos

Background subtraction is a basic task in computer vision and video processing often applied as a pre-processing step for object tracking, people recognition, etc. Recently, a number of successful background-subtraction algorithms have been proposed, however nearly all of the top-performing ones are supervised. Crucially, their success relies upon the availability of some annotated frames of the test video during training. Consequently, their performance on completely “unseen” videos is undocumented in the literature. In this work, we propose a new, supervised, background subtraction algorithm for unseen videos (BSUV-Net) based on a fully-convolutional neural network. The input to our network consists of the current frame and two background frames captured at different time scales along with their semantic segmentation maps. In order to reduce the chance of overfitting, we also introduce a new data-augmentation technique which mitigates the impact of illumination difference between the background frames and the current frame. On the CDNet-2014 dataset, BSUV-Net outperforms stateof-the-art algorithms evaluated on unseen videos in terms of several metrics including F-measure, recall and precision.Accepted manuscrip