quantitative-localization-golgi-protein-imaging-its-center

Quantitative Localization of a Golgi Protein by Imaging Its Center of Fluorescence Mass

The Golgi complex consists of serially stacked membrane cisternae which can be further categorized into sub-Golgi regions, including the cis-Golgi, ...

fully-automated-leg-tracking-freely-moving-insects-using-feature

Fully Automated Leg Tracking in Freely Moving Insects using Feature Learning Leg Segmentation and Tracking (FLLIT)

The Drosophila model has been invaluable for the study of neurological function and for understanding the molecular and cellular mechanisms that underlie ...

Bioinformatics Institute

National University of Singapore

University of Alberta

In this paper, the optimizations of three fundamental components of image understanding: segmentation/annotation, 3D sensing (stereo) and 3D fitting, are posed and integrated within a Bayesian framework. This approach benefits from recent advances in statistical learning which have resulted in greatly improved flexibility and robustness. The first two components produce annotation (region labeling) and depth maps for the input images, while the third module integrates and resolves the inconsistencies between region labels and depth maps to fit most likely 3D models. To illustrate the application of these ideas, we have focused on the difficult problem of fitting individual tree models to tree stands which is a major challenge for vision-based forestry inventory systems.

Component optimization for image understanding: a Bayesian approach.

Structural study of retinal blood vessels provides an early indication of diseases such as diabetic retinopathy, glaucoma, and hypertensive retinopathy. These studies require accurate tracing of retinal vessel tree structure from fundus images in an automated manner. However, the existing work encounters great difficulties when dealing with the crossover issue commonly-seen in vessel networks.

Tracing retinal vessel trees by transductive inference.

A retinal vessel tracking method based on Bayesian theory and multi-scale line detection is proposed in this paper. The optic disk is located by a PCA method and the initial points of tracking are identified. In each step, candidate points for vessel edges are selected on a semi-ellipse. Three types of vessel structure are considered in the tracking: normal vessel, branching, and crossing. To determine the new pair of edge points, the characteristics of the vessel intensity profiles along both the cross section and the longitudinal direction are considered in the tracking. A Gaussian model is assumed in the cross section and multi-scale line detection is employed in the longitudinal direction. The advantage of the proposed method is that two dimensional vessel information is employed, which makes it work better than methods using one dimensional information only. Our method is tested on the REVIEW database and a comparison study is performed. Experimental results show that the proposed method is precise and robust in tracking vessel edges. 

A retinal vessel boundary tracking method based on Bayesian theory and multi-scale line detection.

This paper aims at synthesizing multiple realistic-looking retinal (or neuronal) images from an unseen tubular structured annotation that contains the binary vessel (or neuronal) morphology. The generated phantoms are expected to preserve the same tubular structure, and resemble the visual appearance of the training images. Inspired by the recent progresses in generative adversarial nets (GANs) as well as image style transfer, our approach enjoys several advantages. It works well with a small training set with as few as 10 training examples, which is a common scenario in medical image analysis. Besides, it is capable of synthesizing diverse images from the same tubular structured annotation. Extensive experimental evaluations on various retinal fundus and neuronal imaging applications demonstrate the merits of the proposed approach.

Synthesizing retinal and neuronal images with generative adversarial nets.

Some neurodegenerative diseases, like Parkinsons Disease (PD) and Spinocerebellar ataxia 3 (SCA3), are associated with distinct, altered gait and tremor movements that are reflective of the underlying disease etiology. Drosophila melanogaster models of neurodegeneration have illuminated our understanding of the molecular mechanisms of disease. However, it is unknown whether specific gait and tremor dysfunctions also occur in fly disease mutants. To answer this question, we developed a machine-learning image-analysis program, Feature Learning-based LImb segmentation and Tracking (FLLIT), that automatically tracks leg claw positions of freely moving flies recorded on high-speed video, producing a series of gait measurements. Notably, unlike other machine-learning methods, FLLIT generates its own training sets and does not require user-annotated images for learning. Using FLLIT, we carried out high-throughput and high-resolution analysis of gait and tremor features in Drosophila neurodegeneration mutants for the first time. We found that fly models of PD and SCA3 exhibited markedly different walking gait and tremor signatures, which recapitulated characteristics of the respective human diseases. Selective expression of mutant SCA3 in dopaminergic neurons led to a gait signature that more closely resembled those of PD flies. This suggests that the behavioral phenotype depends on the neurons affected rather than the specific nature of the mutation. Different mutations produced tremors in distinct leg pairs, indicating that different motor circuits were affected. Using this approach, fly models can be used to dissect the neurogenetic mechanisms that underlie movement disorders.

Fully automated leg tracking of Drosophila neurodegeneration models reveals distinct conserved movement signatures.

Diabetic Retinopathy (DR) is the most common cause of avoidable vision loss, predominantly affecting the working-age population across the globe. Screening for DR, coupled with timely consultation and treatment, is a globally trusted policy to avoid vision loss. However, implementation of DR screening programs is challenging due to the scarcity of medical professionals able to screen a growing global diabetic population at risk for DR. Computer-aided disease diagnosis in retinal image analysis could provide a sustainable approach for such large-scale screening effort. The recent scientific advances in computing capacity and machine learning approaches provide an avenue for biomedical scientists to reach this goal. Aiming to advance the state-of-the-art in automatic DR diagnosis, a grand challenge on "Diabetic Retinopathy - Segmentation and Grading" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2018). In this paper, we report the set-up and results of this challenge that is primarily based on Indian Diabetic Retinopathy Image Dataset (IDRiD). There were three principal sub-challenges: lesion segmentation, disease severity grading, and localization of retinal landmarks and segmentation. These multiple tasks in this challenge allow to test the generalizability of algorithms, and this is what makes it different from existing ones. It received a positive response from the scientific community with 148 submissions from 495 registrations effectively entered in this challenge. This paper outlines the challenge, its organization, the dataset used, evaluation methods and results of top-performing participating solutions. The top-performing approaches utilized a blend of clinical information, data augmentation, and an ensemble of models. These findings have the potential to enable new developments in retinal image analysis and image-based DR screening in particular.

IDRiD: Diabetic Retinopathy - Segmentation and Grading Challenge.

The worldwide prevalence of "sensitive skin" group is estimated at being close to 40%. The main trigger for sensitive skin is the misuse of cosmetics products. Majority of the in vitro studies on cosmetic ingredients developed for topical application to the skin are not able to describe sensory irritation, such as stinging, burning, itching, and tingling. Besides, most of the in vivo tests often encounter problems such as limited number of subjects and usage scenarios deviate from reality.

Li Cheng

Bioinformatics Institute

Quantitative Localization of a Golgi Protein by Imaging Its Center of Fluorescence Mass

Fully Automated Leg Tracking in Freely Moving Insects using Feature Learning Leg Segmentation and Tracking (FLLIT)