BioImage InformaticsNODE

France BioImaging develops or supports the development of different software 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.
• BioImageIT: a unique open-source system integrating imaging data management and analysis, and an operational solution for handling large data sets, in line with the requirements of open science.
• Software@Serpico: Try online 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 , running 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.

Every node of France BioImaging has experts in bioimage analysis, that will guide you for your bioImaging 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 

We aim to support the image life cycle from the data production to its archiving through its analysis. We do not provide by ourself resources for all the stages of the image data life cycle, but we can accompany you in identifying such resources. 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 identifying 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  an image data management software, options exist to share your data or part of your data with collaborators, without duplicating the data.

These options 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:

• Using a public image archive; such as bioimage archive  https://www.ebi.ac.uk/bioimage-archive/
• Generalist data deposition https://datadryad.org/stash  or https://zenodo.org/
•  Using your institute or a national node archive if they support metadata and exposition.

 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/