Software

Shareloc

ShareLoc

ShareLoc is a platform to collect, annotate, visualize and reutilize single molecule localization microscopy (SMLM) data (Ouyang, Bai et al., 2022).

ShareLoc is available here: https://shareloc.xyz/#/

Imjoy

Imjoy is a web-based computing platform for deploying advanced image analysis tools such as deep learning (Ouyang et al., 2019).

The door to Imjoy is here: https://imjoy.io/

ZOLA-3D

Zernike Optimized Localization approach

This software allows to reconstruct 3D super-resolution microscopy images obtained using optically engineered point spread functions.

Available at: https://github.com/imodpasteur/ZOLA-3D.

The method is described in detail in Aristov et al. 2018.

3D image of nuclear pores, with color indicating axial position

ANNA-PALM

Artificial neural network accelerated localization microscopy

This software allows to vastly reduce the acquisition time of super-resolution localization microscopy.

Available at https://annapalm.pasteur.fr/#/.

The method is described in detail in Ouyang et al. 2018.

Compressive 3D microscopy

Software for compressive 3D light sheet or epifluorescence microscopy

This software was used to reconstruct 3D images from a series of 2D images obtained using a compressive imaging system, as described in Woringer et al. Optics Express 2017.

Python notebooks are available here: https://github.com/imodpasteur/CompressedSensingMicroscopy3D. Related code for Micromanager and Arduino is available here: https://github.com/imodpasteur/ArduinoCompressedSensing

GRAAL

Software for genome assembly from chromosome contact frequencies

A software to reconstruct 1D genome structures from 3D contact data obtained from Hi-C experiments. Source code and a readme file are available for download here. The computational method is described in Marie-Nelly et al. Nat Comm 2014.

The movie shows the iterative assembly by GRAAL of the Trichoderma reesei genome (right) using contact frequencies determined by the chromosome conformation capture technique (left). Starting from 77 contigs, GRAAL progressively determines 7 chromosomal scaffolds (the end of the movie is not shown).

FISH-quant

Software for automatically counting transcripts in RNA-FISH images

A free Matlab-based software to detect and count individual mRNA transcripts in individual cells by automatic analysis of 3D RNA-FISH images is available freely together with extensive instructions at : https://code.google.com/p/fish-quant/ or https://github.com/imodpasteur/QuickPALM.

The software is described in Mueller et al. Nature Methods (2013).

QuickPALM

Reconstruction software for pointillist super-resolution microscopy

A free and fast ImageJ plugin for reconstructing super-resolution 3D images in PALM/STORM microscopy is available freely on Github (archived repository: http://code.google.com/p/quickpalm/).

This website also offers tutorials about using the software and practical information on hardware issues.

The software is described in Henriques et al. Nature Methods (2010).

Nucloc

Software for 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 non-profit researchers (provided you register and accept our license agreement) at: www.nucloc.org.

The software is at the core of the method described in Berger et al. Nature Methods (2008).