Imaging and Modeling

5 Members

autoFISH : a modular toolbox for sequential FISH experiments

Florian Muller (PI)

We develop a complete workflow to perform automated sequential smFISH experiments on a microscope. This includes building plans for hardware, opens-source control software, and robust experimental protocols for regular and amplified FISH. Lastly, we […]

Deep learning for biology

Deep learning methods use artificial neural networks to learn complex mappings between raw numeric input data and higher order semantic outputs. These computational techniques are at the heart of recent advances in artificial intelligence, with breakthrough […]

6 Members

Pointillist nanoscopy

Fluorescence microscopy is a defining technology in cellular biology but the diffraction of light limits the resolution of standard microscopes to ~200 nm, thus preventing detailed analyses of molecular structures. We are actively interested […]

6 Members

Nuclear architecture and function

The one-dimensional sequence of the genome is carried by long polymers (chromosomes), which fold in the three dimensional volume of the nucleus. How this folding occurs and what it implies for genome function remains […]

Transversal Project

Artificial Intelligence at the Institut Pasteur

Institut Pasteur is actively engaged in the application of artificial intelligence methods in biomedical research. In 2018, the Institute has created a Department of Computational Biology to strengthen its expertise in the analysis of […]

Drug Discovery & Screening at Institut Pasteur

The Technological Targeted Action Drug Discovery and Screening (ATC-DDS) coordinates projects and collaborations at the Institut Pasteur Paris campus on therapeutic development. It raises awareness for DDS in basic research projects and stimulates intra-campus […]

Antimicrobial resistance

Antimicrobial resistance is dramatically increasing worldwide and is becoming one of the most urgent public health threats. There is an urgent need for actions to reverse the curve of antimicrobial resistance dissemination and to […]

Ageing & Longevity

According to the WHO, the global percentage of people aged of more than 60 years will double from 11 to 22% between 2000 and 2050. Nowadays most of the elderly die of non-transmissible diseases […]

INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations

IINCEPTION Goal The Inception aims to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in various health issues (Official website here: https://www.inception-program.fr/en). The inception program uses Integrative Biology, […]

Quantitative biology

The Quantitative Biology program of the Institut Pasteur is intended to facilitate research and education at the interface of biology and the more quantitative sciences. One of the major aims of Quantitative Biology is thus to […]

The institut Carnot Pasteur MS

Carnot, label of excellence Founded in 2006, the Carnot Label, granted by the French government, was designed to develop partnership-based research, meaning research conducted by public laboratories in partnership with socio-economic players, primarily industry […]

Software

FISH-quant v2: a scalable and modular tool for smFISH image analysis

Florian Muller (PI)

Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling quantitative studies of gene expression […]

ZOLA-3D Zernike Optimized Localization approach

This software allows to reconstruct 3D super-resolution microscopy images obtained using optically engineered point spread functions. See Aristov et al. 2018. Available at: https://github.com/imodpasteur/ZOLA-3D.

ANNA-PALM

This software allows to vastly reduce the acquisition time of super-resolution localization microscopy. See https://annapalm.pasteur.fr/#/. The method is described in detail in Ouyang et al. 2018.

6 Members

GRAAL: genome assembly from chromosome contact frequencies

A software to reconstruct 1D genome structures from 3D contact data obtained from Hi-C experiments. This movie shows the iterative assembly by GRAAL of the Trichoderma reesei genome (right) using contact frequencies determined by […]

FISH-quant: automatically counting transcripts in RNA-FISH images

A free Matlab-based toolbox to detect and count individual mRNA transcripts in single cells by automatic analysis of 3D RNA-FISH images. Software is available freely together with extensive instructions at : https://code.google.com/p/fish-quant/. The software […]

QuickPALM: Reconstruction of PALM/STORM super-resolution microscopy images

A free and fast ImageJ plugin for reconstructing super-resolution 3D images in PALM/STORM microscopy is available freely for download at : http://code.google.com/p/quickpalm/This website also offers tutorials about using the software and practical information on […]

Nucloc: mapping gene territories in the yeast nucleus

We have developed a series of software tools to compute and analyze the positions of genomic loci from thousands of yeast cells observed in fluorescence microscopy. These tools are available freely to academic and […]

Tools

Tool