Ahmed S

Superresolution microscopy reveals distinct localisation of full length IRSp53 and its I-BAR domain protein within filopodia

Published date : 21 Feb 2019

Superresolution microscopy offers the advantage of imaging biological structures within cells at the nano-scale. Here we apply two superresolution microscopy techniques, specifically 3D structured illumination microscopy (3D-SIM) and direct stochastic optical reconstruction microscopy (dSTORM), a type of single molecule localisation microscopy, to localise IRSp53 protein and its I-BAR domain in relation to F-actin within filopodia. IRSp53 generates dynamic (extending and retracting) filopodia 300 nm wide with a distinct gap between IRSp53 and F-actin.

type
Journal Paper
journal
Scientific Reports 9, Article no: 2524(2019). doi: 10.1038/s41598-019-38851-w
Impact Factor
4.122

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

Light sheet fluorescence microscopy (LSFM): past present and future

Published date : 21 Jul 2014

Light sheet fluorescence microscopy (LSFM) has emerged as an important imaging modality to follow biology in live 3D samples over time with reduced phototoxicity and photobleaching. In particular, LSFM has been instrumental in revealing the detail of early embryonic development of Zebrafish, Drosophila, and C. elegans. Open access projects, DIY-SPIM, OpenSPIM, and OpenSPIN, now allow LSFM to be set-up easily and at low cost. The aim of this paper is to facilitate the set-up and use of LSFM by reviewing and comparing open access projects, image processing tools and future challenges.

type
Journal Paper
journal
Analyst, 2014, Issue 139, pg 4758-4768, doi: 10.1039/C4AN00624K
Impact Factor
3.969

An Analysis-Synthesis Approach for Neurosphere Modelisation Under Phase-Contrast Microscopy

Published date : 03 Jul 2013

The study of stem cells is one of the most important biomedical research. Understanding their development could allow multiple applications in regenerative medicine. For this purpose, automated solutions for the observation of stem cell development process are needed. This study introduces
an on-line analysis method for the modelling of neurosphere evolution during the early time of their development under phase contrast microscopy. From the corresponding phase contrast time-lapse sequences, we extract information from the neurosphere using a combination of phase contrast physics

type
Conference Paper/Poster
journal
35th Annual International Conference of the IEEE Engineering in Medicine and Biology Socity, 3-7 July, 2013, Osaka, Japan

Segmentation of Unstained Neural Stem Cells/Neurospheres in Unevenly Illuminated Brightfield Images with Shading Reduction

Published date : 11 Nov 2012

Imaging unstained neural stem cells/ neurospheres using low magnification brightfield modality results in uneven illumination effects across the field of view. Globally, the centre appears bright while the edges appear dark; locally, illumination varies across individual adjacent site images. Furthermore, neurospheres residing in the dark background regions have low signal noise ratio. Altogether, they impose challenges for automated computer vision analysis. We propose a method which reduces the shading effects by formulating estimated global and local illumination models.

type
Conference Paper/Poster
journal
21st International Conference on Pattern Recognition, 11 to 15 Nov 2012, Tsukuba Science City, Japan

Segmentation of Neural Stem Cells/Neurospheres in High Content Brightfield Microscopy Images Using Localized Level Sets

Published date : 30 Sep 2012

Neural stem cells and neural progenitors are early nervous system cells that form neurospheres when propagated in vitro. We study changes in growth using brightfield images to understand the effects of drugs. The image quality is generally poor, imposing challenges for automatic analysis. Level-set segmentation methods are able to handle topology changes but require close initializations for accurate and efficient results. Global level-set methods using single image-wide optimization objective functions are difficult to cope with large illumination and shading changes.

type
Conference Paper/Poster
journal
2012 IEEE International Conference on Image Processing, 30 Sep - 3 Oct 2012, Florida, USA

On-line 3-D Tracking of Suspension Living Cells Imaged with Phase-Contrast Microscopy

Published date : 11 Apr 2012

Neural stem cells/neural progenitors (NSCs/NPs) are cells that give rise to the main cell types of the nervous system: oligodendrocytes, neurons, and astrocytes. Studying NSCs/NPs with time-lapse microscopy is critical to the understanding of the biology of these cells. However, NSCs/NPs are very sensitive to phototoxic damage, and therefore, fluorescent dyes cannot be used to follow these cells. Also, since in most of NSC/NP-related experiments, a large number of cells neesd to be monitored. Consequently, the acquisition of a huge amount of images is required.

type
Journal Paper
journal
IEEE Transactions on Biomedical Engineering, July 2012, Vol. 59, Issue 7, Pg 1924-1933, doi : 10.1109/TBME.2012.2194487

Accurate single-molecule localization of superresolution microscopy images using multiscale products

Published date : 13 Feb 2012

Recently, a class of single-molecule based localization techniques such as the Photo-activated Localization Mi- croscopy (PALM) or the Stochastic Optical Reconstruction Microscopy (STORM) has ingeniously brought light- microscopy beyond the diraction limit. However, as the single-molecule images contain point source objects (which have no clear edges, alignment and usually superimposed to the background), traditional restoration techniques used for industrial vision images do not give satisfactory result on the PALM/STORM dataset.

type
Conference Paper/Poster
journal
Proceedings of SPIE Volume 8228 (2012), doi: 10.1117/12.907221