Image Processing & Data Management transversal node

The objective of the BioImage Informatics – Image Processing & Data Management transversal node is to create a general framework and a complete and integrated image analysis and IT (Information Technology) solution to address a number of challenges in biological imaging and microscopy, as well as setting up a high performance grid-computing infrastructure dedicated to massive computational and data storage demands. The FBI-IPDM node proposes different IT frameworks to deal with the data flow from the different imaging nodes. FBIIPDM node is thus transverse, by definition.

Numbers in 2018

  • active users of our software platform
  • international conference participation
  • software copyright deposit

Image Processing & Management Software

  • Icy Software Platform
  • Mobyle@Serpico
  • Open Mole@BioEmergences
  • OpenImadis
© Adrien Demilly - Institut Jacques Monod

Our Main Projects

  • France BioImaging Open Data Repository – OpenImadis
  • Metrology Annotations for Data Bases
  • Training initiatives at the national & European levels
Facility

BioEmergences

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Facility: BioEmergences

Head: Nadine Peyréras

Université Paris-Sud, Rue Georges Clemenceau, Orsay, France

 The BioEmergences platform (UPS in 2014) develops, applies to specific case studies, and offers as services, original methodologies and tools for the multi-scale phenomenological and theoretical reconstruction of the development of model organisms, animal or vegetal. The work is organized along the lines of an applied epistemology that we defined in the context of the Institute for Complex Systems which is part of the national and international roadmap established by the Complex Systems community http://roadmaps.csregistry.org/. We developed a workflow going from photonic microscopy for in vivo and in toto imaging of developing organisms to the automated reconstruction of 3D+time data, analysis of digital specimens and modeling of morphogenetic processes. In this context provide collaborative services that most of the time, correspond to new challenging applications (WP1b, WP1d, WP2, WP3). FBI funding is used to develop a so-called artificial assistant based on a SPIM or MLMS imaging concept with real time image processing and feedback on the imaging scheme. All our activity involves image processing (WP4), that’s why we are involved in IPDM node too. We expect to provide the community with original webservices to access the BioEmergences reconstruction workflow and grid computing.

Services on this Facility

Service

Image Data Handling

Service

Microscopy Technologies

Facility

Institut Curie – Bioimage Informatics IPDM

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Facility: Institut Curie – Bioimage Informatics IPDM

Head: Perrine Paul-Gilloteaux

Institut Curie - Pavillon Trouillet-Rossignol, Rue d'Ulm, 5e Arrondissement, France

Institut Curie is active in image databases and management. The PICT imaging facility is engaged since 2011 with the Strand Life Sci. company in the development of the CID (Curie Image Database)/iManage (supported by Paris-Centre Node). The CID is linked to the “Curie Image Data center” (2x 100Tb Storage equipment and cluster for image processing and analysis). Since December 2013 CID is open to all FBI users of the PICT, under demand and common rules of imaging platforms (web client). iManage is the commercial version (with licensing), offering support to labs, to install and adapt CID on their own microscopy, at their own sites. Plugins to access the CID from Icy (Institut Pasteur) are developed and published on the central repository of Icy. An interface to interoperate with the servers at Institut Curie is under development. Integration of software developed in collaboration with Inria-Serpico (http://mobyleserpico.rennes.inria.fr/) such as ND-SAFIR, Hullkground are now integrated in the CID for automated treatment. Institut Curie, specifically with Serpico’s Team@Inria-Rennes, also develops new algorithm solutions for dynamic events detection and classification, sub-diffraction light microscopy and CLEM approaches.

Facility

Image Analysis Hub – Institut Pasteur

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Facility: Image Analysis Hub – Institut Pasteur

Head: Jean-Yves Tinevez

iah@pasteur.fr
Institut Pasteur, Paris, France

About

The Image Analysis Hub is an open access, equal access core facility committed to offering support in image analysis. Our webpage is: https://research.pasteur.fr/en/team/image-analysis-hub/

What we do.

As part of the C2RT, we strive to ensure the continuity between image acquisition and image analysis. To this end we rely on our expertise in imaging and collaborate with other facilities such as the UTechS-PBI and UTechS-UBI when pertinent. All requests involving images are considered.

 

Our services follow four axes:

1. Offer walk-in support and trainings for questions involving image analysis.

This activity aims at offering to users quick answers to scientific questions involving well-established pipelines, for which a commercial or published tool exists and can be used conveniently. Users can address their question to the facility during open-desk sessions or directly via one-to-one requests. Depending on the effort involved, the solution is derived and proposed onsite, or individual  trainings are scheduled. For general topics, the Hub organises regular courses and workshops, possibly involving external teachers or providers.

For instance, see below for the announcement of our open-desk, organised regularly every two week.

 

2. Build and deploy custom analysis tools for projects requiring special developments.

Research endeavours to address original questions, for which analysis tools might be lacking or incomplete. The Image Analysis Hub aims at creating or implementing novel tools based on existing algorithms to address these questions, using skills in image analysis and software development. More than just developing the analysis tool, this activity often involves deriving a suitable analysis methodology, for which the facility expertise in microscopy and biophysics is key. Engineers work in close collaboration with users within the framework of a scientific project over medium or long durations. For projects whose effort would extend beyond typical facility usage or involve original research work, the project may be directed to the BioImage Analysis unit after a discussion with all parts.

 

3. Maintain an infrastructure for autonomous image analysis. Deal with complex tool deployments.

Data volume and modern analysis techniques may call for a computing power not always present in Pasteur labs. Providing open-access workstations unlock barriers to compute-intensive tools. They also act as the central sharing points for commercial softwares, making them available to the whole campus. Finally, some specialized tools require special deployment efforts, e.g. to make such a tool able to exploit the HPC infrastructure of the Institut Pasteur.

 

4. Develop original and innovative software tools for image analysis, whose scope exceed user projects.

Software development and image analysis skills of the facility can be leveraged to build ambitious software tools shipping innovative technologies. These tools exceed the scope of single projects and address the unarticulated needs of the Pasteur community and their creation is part of the development activity of the facility.

Services on this Facility

Service

Image Data Handling

R&D team

Team Montpellier-IPDM-MRI & MARS

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R&D team: Team Montpellier-IPDM-MRI & MARS

Head: Marcelo Nollmann

Université Montpellier 1, Montpellier, France

The team is working on a data and image management software. Its main purpose is the management of the data created by the resources of the facility that are driven by a computer (for example microscopes and flow cytometers). All data acquired on the machines of the facility can be uploaded into WIDE. They can then easily be managed on the website, using any computer that has an internet connection. MARS is working on improving a local storage solution and computing for the user’s data.

R&D team

Institut Pasteur – BioImage Analysis Team

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R&D team: Institut Pasteur – BioImage Analysis Team

Head: Jean-Christophe Olivo-Marin

jean-christophe.olivo-marin@pasteur.fr
Institut Pasteur, Rue du Docteur Roux, Paris, France

The scientific project of the BioImage Analysis (BIA) unit is to develop image analysis and computer vision tools for the processing and quantification of multi-channel temporal 3D sequences in biological microscopy. The topics are centered about the development of new algorithms for multi-particle tracking, deformable models, mathematical imaging and spatial distribution analysis. The group has produced powerful tools for spot detection and counting in real-time imaging of virus and genes, movement and shape analysis in 3D+t microscopy and cell growth analysis. These methods and algorithms have now been regrouped under the open-source and free platform Icy (http://icy.bioimageanalysis.org), which provides a comprehensive framework for extended reproducible research in bioimage informatics. They have been instrumental for the successful achievement of a large number of collaborative biological projects.

Services on this R&D team

Service

Image Data Handling

R&D team

Inria-Serpico

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R&D team: Inria-Serpico

Head: Charles Kervrann

Inria Rennes - Bretagne Atlantique, Avenue Général Leclerc, Rennes, France

The Serpico team provides computational methods and mathematical models to automatically extract, organize and model information present in temporal series of images as they are obtained in multidimensional light and cryo-electron microscopy. In the field of membrane traffic, Serpico addresses the following themes in close collaboration with Curie Institute: image superresolution and image denoising to preserve cell integrity (photo-toxicity vs exposure time), information extraction from images and videos in multidimensional microscopy for molecular interaction analysis, spatiotemporal modeling of molecular species and multi-scale architectures, computational simulation and modeling of membrane transport at different scales. In collaboration with UMR 144 and PICT at Institut Curie, the members of Serpico participate in several joint projects (PhD and post-doc supervision, industrial contracts…). They have proposed user-friendly algorithms for processing 3D or 4D data. Other projects are related to instrumentation in microscopy including computational aspects (SERPICO@Mobyle web service) and data management (CID iManage) on the reconstruction and enhancement of images related to subdiffraction light microscopy and multimodal approaches.

Services on this R&D team

Service

Image Data Handling