BOUDIER Thomas

A novel toolbox to investigate tissue spatial organization applied to the study of the islets of Langerhans

Thanks to the development of new 3D Imaging techniques, volumetric data of thick samples, especially tissues, are commonly available. Several algorithms were proposed to analyze cells or nuclei in tissues, however these tools are limited to two dimensions. Within any given tissue, cells are not likely to be organized randomly and as such have specific patterns of cell-cell interaction forming complex communication networks. In this paper, we propose a new set of tools as an approach to segment and analyze tissues in 3D with single cell resolution.

type: 
Journal Paper
journal: 
Scientific Reports 7, Article number: 44261 (2017), doi:10.1038/srep44261
Url: 
http://www.nature.com/articles/srep44261
Impact Factor: 
5.228
Date of acceptance: 
2017-02-07

Optimal processing for gel electrophoresis images: Applying Monte Carlo Tree Search in GelApp

In biomedical research, gel band size estimation in electrophoresis analysis is a routine process. To facilitate and automate this process, numerous software have been released, notably the GelApp mobile app. However, the band detection accuracy is limited due to a band detection algorithm that cannot adapt to the variations in input images. To address this, we used the Monte Carlo Tree Search with Upper Confidence Bound (MCTS-UCB) method to efficiently search for optimal image processing pipelines for the band detection task, thereby improving the image processing algorithm.

type: 
Journal Paper
journal: 
Electrophoresis 2016, 10.1002/elps.201600197
Url: 
http://onlinelibrary.wiley.com/doi/10.1002/elps.201600197/full
Impact Factor: 
3.028
Date of acceptance: 
2016-05-23

Optimal processing for gel electrophoresis images: Applying Monte Carlo Tree Search in GelApp

In biomedical research, gel band size estimation in electrophoresis analysis is a routine process. To facilitate and automate this process, numerous software have been released, notably the GelApp mobile app. However, the band detection accuracy is limited due to a band detection algorithm that cannot adapt to the variations in input images. To address this, we used the Monte Carlo Tree Search with Upper Confidence Bound (MCTS-UCB) method to efficiently search for optimal image processing pipelines for the band detection task, thereby improving the image processing algorithm.

type: 
Journal Paper
journal: 
Electrophoresis 2016, 10.1002/elps.201600197
pubmed: 
http://onlinelibrary.wiley.com/doi/10.1002/elps.201600197/full
Url: 
http://onlinelibrary.wiley.com/doi/10.1002/elps.201600197/full
Impact Factor: 
2.482
Date of acceptance: 
2016-06-20

OpenSegSPIM: a user-friendly segmentation tool for SPIM data

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
Url: 
http://bioinformatics.oxfordjournals.org/content/early/2016/02/22/bioinformatics.btw093.abstract
Impact Factor: 
4.981
Date of acceptance: 
2016-02-14

Biomineralization Patterns of Intracellular Carbonatogenesis in Cyanobacteria: Molecular Hypotheses

The recent discovery of intracellular carbonatogenesis in several cyanobacteria species
has challenged the traditional view that this process was extracellular and not controlled. However,
a detailed analysis of the size distribution, chemical composition and 3-D-arrangement of carbonates
in these cyanobacteria is lacking. Here, we characterized these features in Candidatus Gloeomargarita
lithophora C7 and Candidatus Synechococcus calcipolaris G9 by conventional transmission electron
microscopy, tomography, ultramicrotomy, and scanning transmission X-ray microscopy (STXM).

type: 
Journal Paper
journal: 
Minerals 2016, 6(1), 10; doi:10.3390/min6010010
Url: 
http://www.mdpi.com/2075-163X/6/1/10
Date of acceptance: 
2016-01-25

Progerin reduces LAP2α-telomere association in Hutchinson-Gilford progeria

Hutchinson-Gilford progeria (HGPS) is a premature ageing syndrome caused by a mutation in LMNA, resulting in a truncated form of lamin A called progerin. Progerin triggers loss of the heterochromatic marker H3K27me3, and premature senescence, which is prevented by telomerase. However, the mechanism how progerin causes disease remains unclear. Here, we describe an inducible cellular system to model HGPS and find that LAP2α (lamina-associated polypeptide-α) interacts with lamin A, while its interaction with progerin is significantly reduced.

type: 
Journal Paper
journal: 
Elife 2015 Aug 27;4. doi: 10.7554/eLife.07759
pubmed: 
26312502
Url: 
http://elifesciences.org/content/4/e07759
Impact Factor: 
9.322
Date of acceptance: 
2015-08-23
Syndicate content