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Projects

project
Ongoing
2 Members

Deep learning for biology

Christophe Zimmer (PI)

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 […]
project
Ongoing
10 Members

Pointillist nanoscopy

Christophe Zimmer (PI)

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 […]
project
Ongoing
10 Members

Nuclear architecture and function

Christophe Zimmer (PI)

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 […]

Software

software
Ongoing
2 Members

ZOLA-3D Zernike Optimized Localization approach

Christophe Zimmer (PI)

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.
software
Completed
2 Members

ANNA-PALM

Christophe Zimmer (PI)

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.
software
Completed
6 Members

GRAAL: genome assembly from chromosome contact frequencies

Christophe Zimmer (PI)

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 […]
software
Completed
2 Members

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

Christophe Zimmer (PI)

  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
Completed
2 Members

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

Christophe Zimmer (PI)

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 […]
software
Completed
2 Members

Nucloc: mapping gene territories in the yeast nucleus

Christophe Zimmer (PI)

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 […]

Publications

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