Particle detection and tracking in fluorescence time-lapse imaging: a contrario approach

This paper proposes a probabilistic approach for the detection and the tracking of particles in fluorescent time-lapse imaging. In the presence of a very noised and poor-quality data, particles and trajectories can be characterized by an a contrario model, that estimates the probability of observing the structures of interest in random data. This approach, first introduced in the modeling of human visual perception and then successfully applied in many image processing tasks, leads to algorithms that neither require a previous learning stage, nor a tedious parameter tuning and are very robust to noise. Comparative evaluations against a well-established baseline show that the proposed approach outperforms the state of the art.Comment: Published in Journal of Machine Vision and Application

Veni Vidi Vici, A Three-Phase Scenario For Parameter Space Analysis in Image Analysis and Visualization

Automatic analysis of the enormous sets of images is a critical task in life sciences. This faces many challenges such as: algorithms are highly parameterized, significant human input is intertwined, and lacking a standard meta-visualization approach. This paper proposes an alternative iterative approach for optimizing input parameters, saving time by minimizing the user involvement, and allowing for understanding the workflow of algorithms and discovering new ones. The main focus is on developing an interactive visualization technique that enables users to analyze the relationships between sampled input parameters and corresponding output. This technique is implemented as a prototype called Veni Vidi Vici, or "I came, I saw, I conquered." This strategy is inspired by the mathematical formulas of numbering computable functions and is developed atop ImageJ, a scientific image processing program. A case study is presented to investigate the proposed framework. Finally, the paper explores some potential future issues in the application of the proposed approach in parameter space analysis in visualization

Morphological segmentation analysis and texture-based support vector machines classification on mice liver fibrosis microscopic images

Background To reduce the intensity of the work of doctors, pre-classification work needs to be issued. In this paper, a novel and related liver microscopic image classification analysis method is proposed. Objective For quantitative analysis, segmentation is carried out to extract the quantitative information of special organisms in the image for further diagnosis, lesion localization, learning and treating anatomical abnormalities and computer-guided surgery. Methods in the current work, entropy based features of microscopic fibrosis mice’ liver images were analyzed using fuzzy c-cluster, k-means and watershed algorithms based on distance transformations and gradient. A morphological segmentation based on a local threshold was deployed to determine the fibrosis areas of images. Results the segmented target region using the proposed method achieved high effective microscopy fibrosis images segmenting of mice liver in terms of the running time, dice ratio and precision. The image classification experiments were conducted using Gray Level Co-occurrence Matrix (GLCM). The best classification model derived from the established characteristics was GLCM which performed the highest accuracy of classification using a developed Support Vector Machine (SVM). The training model using 11 features was found to be as accurate when only trained by 8 GLCMs. Conclusion The research illustrated the proposed method is a new feasible research approach for microscopy mice liver image segmentation and classification using intelligent image analysis techniques. It is also reported that the average computational time of the proposed approach was only 2.335 seconds, which outperformed other segmentation algorithms with 0.8125 dice ratio and 0.5253 precision

Image informatics strategies for deciphering neuronal network connectivity

Brain function relies on an intricate network of highly dynamic neuronal connections that rewires dramatically under the impulse of various external cues and pathological conditions. Among the neuronal structures that show morphologi- cal plasticity are neurites, synapses, dendritic spines and even nuclei. This structural remodelling is directly connected with functional changes such as intercellular com- munication and the associated calcium-bursting behaviour. In vitro cultured neu- ronal networks are valuable models for studying these morpho-functional changes. Owing to the automation and standardisation of both image acquisition and image analysis, it has become possible to extract statistically relevant readout from such networks. Here, we focus on the current state-of-the-art in image informatics that enables quantitative microscopic interrogation of neuronal networks. We describe the major correlates of neuronal connectivity and present workflows for analysing them. Finally, we provide an outlook on the challenges that remain to be addressed, and discuss how imaging algorithms can be extended beyond in vitro imaging studies