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-Bio image Informatics node proposes different IT frameworks to deal with the data flow from the different imaging nodes. FBI Bio Image Informatics node is thus transverse, by definition.

What is Bio Image Informatics?

It has been defined as the [field of ] “developing novel image processing, data mining, database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problem” [deluge of molecular and cellular microscopic images] Peng, H, Bioinformatics 2008

What is Bio Image Analysis?

The task of bioimage analysis, part of bio image informatics, is to “ enable [computers] to automatically distinguish between relevant and irrelevant image information and to recognize and model spatial or temporal patterns of interest that could confirm or refute the hypotheses underlying the given experiment through quantitative analysis.” Meijering, E et al. Nature Biotechnology , 2016

Contact: bioimageanalysts@france-bioimaging.org

Node services:

Help yourself: Image Processing & Management Software

Open Help Desk: Ask for help!

Data Management: Plan your data management

 

Numbers in 2018

  • 169 User image analysis projects supported by IPDM staff
  • 2500 Self usage by users of IPDM software (download or on-line access to software)
  • 197 Users trained on image analysis software

Help yourself: Image Processing & Management Software

France BioImaging develops or supports the development of different sofwtare tools that you can download or access on-line :

  • Icy Software Platform : open source bioimaging software package that aims to provide a framework for authors to share, and others to reproduce, research once the sample hits the microscope.
  • Software@Serpico: Try on line through a web server a set of software running on a cluster at Inria.
  • BioEmergences: Track nuclei and membranes workflow, available as a standalone software to download or as webservice , unning on the European Grid Infrastructure using OpenMole.
  • OpenImadis: Open Image Discovery (openImaDis) is an enterprise-wide image and analysis management software platform for Bio-Imaging researchers. It provides shared, secure, uniform and open access to image life cycle data and algorithms. It facilitates effective management of heterogeneous images and complex analysis workflows.
Useful Links:

biii.eu: Bio Image Informatics Inventory List of software Tools, curated by NEUBIAS COST CA15124, network of bio image analysts.

Open Help Desk: Ask for help!

Every node of France Bio Imaging has experts in bio image analysis, that will guide you for your bio Imaging project with three different levels according to the level of complexity of your project:

  1.  Advice on existing Tools that will answer your question, and help in the definition of your analysis workflow and possible biases.
  2. Realisation of your tailored analysis workflow  (constructing a ready to use analysis workflow based on the combination and/or adaptation of existing Tools)
  3. Putting you in contact with the most adapted image processing and analysis R&D Partner teams if the need for a new algorithm has been identified.

For any of this levels, the entry point is  to send an email at bioimageanalysts@france-bioimaging.org or to join us at one of our Open Desk. The calendar of the next open desk is displayed below. For users of the infrastructure without physical access to one of node, a virtual room is open once a month, where image analysts will analyse the category to which your project belong.

Paris Centre node has regular open desk event through the Image Analysis Hub @Pasteur 

Data Management: Plan your data management

We aim to support the image life cycle from the data production to its archiving through its analysis. We do not provide by ourself ressources for all the stages of the image data life cycle, but we can accompany you in indentifying such ressources. Data management plans are becoming an essential part of any scientific project preparation. Because of the explosion of the information content in our microscopy images, but also of their size, it is now mandatory to have a clear vision (plan) about where , when and how data will be handled at the different stages of their life.

The life cycle of image data can be simplified in the different following steps: images acquisition, image processing and analysis, sharing and publishing/archiving .

  • At the level of Image Acquisition

The important information linked to the acquisition, the biological study and the sample imaged need to be stored and associated to the images (Annotations= metadata). Annotations can also comes from metrology for example (quality check).

For this images can be stored in FBI nodes or in your own institution using image data software management system such as OMERO or OpenImadis. We recommend OMERO because of its compatibility with public archives.

Controlled vocabularies (or ontology ) should be used, even if specific to the project. In the useful link below you will find a link to help you indentifying the ontology you may used.

  • At the level of Image Processing and Analysis

Use reproducible image analysis : using script, macros, or visual protocols in ICY for example are a good practice: this will allow to store and save your analysis pipeline as well as the parameters used in a light text file or xml file. Most modern software (such as ICY) also store the exact version of the plugin used.

  • Sharing your data

When you have use  a image data management sofware, options exist to share your data or part of your data with collaborators, without duplicating the data.

These option will also allow you to share the data with Anonymous users as well, for example for the review process of your publication supported by these imaging data.

Example: cid.curie.fr, Omero Marseille, Omero Montpellier 

  • Publishing and Archiving

Most of the publisher or project funded with public money will ask you to make your supporting data permanently accessible . Several options are available:

 Note that in all these solutions you have to make sure that your data will be shared FAIRly, meaning “Findable Accessible Interoperable Reusable”  

Useful Links:

FAIR Principles and metrics:  https://www.go-fair.org/fair-principles/

DMP editors: https://dmp.opidor.fr/

Looking for an ontology: https://bioportal.bioontology.org/

Looking for a public database:

Each node of FBI may propose a public archive:

cid.curie.fr

https://fairsharing.org/

Euro- Bioimaging collection: https://fairsharing.org/collection/EuroBioImaging

https://www.ebi.ac.uk/bioimage-archive/

https://idr.openmicroscopy.org/tissue/

https://idr.openmicroscopy.org/cell/

https://www.ebi.ac.uk/pdbe/emdb/empiar/deposition/login/?next=/pdbe/emdb/empiar/deposition/

Facility

BioEmergences

↗ Website + Info

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

↗ Website ↗ Service + Info

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.

Services on this Facility

Service

Image Data Handling

Facility

Image Analysis Hub – Institut Pasteur

↗ Website + Info

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

↗ Website + Info

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

↗ Website + Info

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-Curie SERPICO/STED

↗ Website ↗ Service + Info

R&D team: Inria-Curie SERPICO/STED

Head & CoHead: Charles Kervrann & Jean Salamero

charles.kervrann@inria.fr
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