Ong Kok Haur

Quantitative 3D analysis of complex single border cell behaviors in coordinated collective cell migration

Published date : 04 Apr 2017

Understanding the mechanisms of collective cell migration is crucial for cancer metastasis, wound healing and many developmental processes. Imaging a migrating cluster in vivo is feasible, but the quantification of individual cell behaviours remains challenging. We have developed an image analysis toolkit, CCMToolKit, to quantify the Drosophila border cell system. In addition to chaotic motion, previous studies reported that the migrating cells are able to migrate in a highly coordinated pattern.

type
Journal Paper
journal
Nature Communications, 2017 Apr 4;8:14905. doi: 10.1038/ncomms14905
Impact Factor
12.124

NeuronCyto II: An Automatic and Quantitative Solution for Crossover Neural Cells in High Throughput Screening

Published date : 27 May 2016

Microscopy is a fundamental technology driving new biological discoveries. Today microscopy allows a large number of images to be acquired using, for example, High Throughput Screening (HTS) and 4D imaging. It is essential to be able to interrogate these images and extract quantitative information in an automated fashion. In the context of neurobiology, it is important to automatically quantify the morphology of neurons in terms of neurite number, length, branching and complexity, etc.

type
Journal Paper
journal
Cytometry A, Vol. 89, Issue 8, Aug 2016, Pg 747-754 doi: 10.1002/cyto.a.22872
Impact Factor
3.066

OpenSegSPIM: a user-friendly segmentation tool for SPIM data

Published date : 22 Feb 2016

OpenSegSPIM is an open access and user friendly 3-D automatic quantitative analysis tool for Single Plane Illumination Microscopy (SPIM) data. The software is designed to extract, in a user friendly way, quantitative relevant information from SPIM image stacks, such as the number of nuclei or cells. It provides quantitative measurement (volume, sphericity, distance, intensity) on Light Sheet Fluorescent Microscopy (LSFM) images.

type
Journal Paper
journal
Bioinformatics, 2016, doi: 10.1093/bioinformatics/btw093
Impact Factor
4.981

A Graph-theoretical Approach for Tracing Filamentary Structures in Neuronal and Retinal Images

Published date : 24 Aug 2015

The aim of this study is about tracing filamentary structures in both neuronal and retinal images. It is often crucial to identify single neurons in neuronal networks, or separate vessel tree structures in retinal blood vessel networks, in applications such as drug screening for neurological disorders or computeraided diagnosis of diabetic retinopathy. Both tasks are challenging as the same bottleneck issue of filament crossovers is commonly encountered, which essentially hinders the ability of existing systems to conduct large-scale drug screening or practical clinical usage.

type
Journal Paper
journal
IEEE Transactions on Medical Imaging, DOI 10.1109/TMI.2015.2465962, vol.35, pp.1-17, 2015
Impact Factor
3.39