Current: Research -- Recent Work

RECENT WORK

Non-invasive single-cell morphometry in living bacterial biofilms

In this work, we present Bacterial Cell Morphometry 3D (BCM3D), an image analysis workflow that combines deep learning with mathematical image analysis to accurately segment and classify single bacterial cells in 3D fluorescence images...Code available!

SITUP: Scale Invariant Tracking using Average Peak-to-Correlation Energy

Robust and accurate scale estimation of a target object is a challenging task in visual object tracking. We propose to incorporate a novel criterion called the average peak-to-correlation energy into the multi-resolution translation filter framework to obtain robust and accurate scale estimation...Code available!

FAST: Fast and Accurate Scale Estimation for Tracking

We propose a scale searching scheme that obtains robust and accurate scale estimation by incorporating a novel and robust criterion, the average peakto-correlation energy, into a multi-resolution translation filter framework...Code available!

NeuroPath2Path: Classification and elastic morphing between neuronal arbors using path-wise similarity

The shape and connectivity of a neuron determine its function. Modern imaging methods have proven successful at extracting such information. NeuroPath2Path is an effective application for neuronal morphological representation. The morphology of a neuron, which consists of its overall size, global shape, local branch patterns...

GlidarCo: gait recognition by 3D skeleton estimation and biometric feature correction of flash lidar data

A flash lidar can provide new opportunities for gait recognition; however, the lower quality and noisy imaging process of flash lidar negatively affects the performance of conventional solutions including the state-of-the-art skeleton-based systems. We present a filtering mechanism that corrects noisy and missing skeleton joint measurements to improve gait recognition ...( See more about the project)

Hieroglyph: Hierarchical Glia Graph Skeletonization and Matching

Automatic 3D reconstruction of glia morphology is a powerful tool necessary for investigating the role of microglia in neurological disorders in the central nervous system. We propose Hieroglyph, a fully automatic temporal 3D skeleton reconstruction algorithm for glia imaged via 3D multiphoton microscopy...

LCuts: Linear Clustering of Bacteria using Recursive Graph Cuts

A graph-based data clustering method, LCuts, is presented with the application on bacterial cell segmentation. The method assists in the assessment of several facets, such as bacterium tracking, cluster growth, and mapping of migration patterns of bacterial biofilms...

Segmentation of Cortical Spreading Depression Wavefronts Through Local Similarity Metric

we present a novel region-based segmentation method for cortical spreading depressions in 2-photon microscopy images. Fluorescent microscopy has become an important tool in neuroscience, but segmentation approaches are challenged by the opaque properties and structures of brain tissue...

PrecoG: an efficient unitary split preconditioner for the transform-domain LMS filter via graph Laplacian regularization

PrecoG is an algorithm that derives a preconditioner for LMS filters. The preconditioner is data-dependent and is designed by modeling the input data with graph topology. It is also prove effective for solving ill-conditioned linear systems and...

Latest advances in image processing for single particle analysis by electron cryomicroscopy and challenges ahead

In this article, we touch on the most essential image processing challenges in order to build an accurate structural three-dimensional model from noisy projection images....

Functional aspects of meningeal lymphatics in ageing and Alzheimer’s disease

A software package developed in-house, Lymph4D (software available online), was used to process and analyse the images acquired by MRI...

ElasticPath2Path: Automated morphological classification of neurons by elastic path matching

In the study of neurons, morphology influences function. The complexity in the structure of neurons poses a challenge in the identification and analysis of similar and dissimilar neuronal cells...(Code)

The Coupled TuFF-BFF Algorithm for Automatic 3D Segmentation of Microglia

We propose an automatic 3D segmentation algorithm for multiphoton microscopy images of microglia. Our method is capable of segmenting tubular and blob-like structures from noisy images...

OSLO: Automatic Cell Counting and Segmentation for Oligodendrocyte Progenitor Cells

Reliable cell counting and segmentation of oligodendrocyte progenitor cells (OPCs) are critical image analysis steps that could potentially unlock mysteries regarding OPC function during pathology....

Nonlinear Shape Regression For Filtering Segmentation Results From Calcium Imaging

A shape filter is presented to repair segmentation results obtained in calcium imaging of neurons in vivo. This post-segmentation algorithm can automatically smooth the preliminary segmentations, while excluding the incomplete segmentations...

SDL: Saliency-Based Dictionary Learning Framework for Image Similarity

In image classification, obtaining adequate data to learn a robust classifier has often proven to be difficult in several scenarios. Classification of histological tissue images for health care analysis is a notable application in this context due to the necessity of surgery, biopsy or autopsy...

Speckle removal and change preservation by distance-driven anisotropic diffusion of synthetic aperture radar temporal stacks

We propose a method that smoothes spatially and uses, but also preserves, temporal information of synthetic aperture radar image stacks. Code available on Github...

Bact-3D: A level set segmentation approach for dense multi-layered 3D bacterial biofilms

This paper presents Bact-3D, a 3D method for segmenting super-resolution images of multi-leveled, living bacteria cultured in vitro. The method incorporates a novel initialization approach that exploits the geometry of the bacterial cells as well an iterative local level set evolution that is tailored to the biological application...