Developed by the Serpico Inria-CNRS-Institut Curie Joint Team, member of the IPDM-BioImage Informatics node of France-BioImaging (FBI), this open-source framework could be a huge step forward in bioimaging management and analysis.

Bioimaging has a broad range of applications, addressing a variety of biological models at diverse scales of life. Thus, descriptions of novel computational approaches are often focused on target case studies. To tackle any scenario in biological imaging is a major challenge, that needs the conception and the development of a unified solution.

With this in mind, the BioImageIT project aims at providing a middleware that integrates data management with analysis using existing softwares (Omero, BioFormats, Fiji, napari, Scipy, pytorch…). The mission of BioImageIT was to design a graphical user interface (GUI) that allows any scientist without coding skills to annotate and analyze datasets using various software. By being user-centered, open-source and cross-platform (Windows, MacOS, Linux), BioImageIT created a management tool that is definitely accessible and well documented.

Started in late 2019, the project, funded by France-BioImaging, is now being deployed in 10 FBI imaging facilities. As it is a first step, the BioImageIT project have the ambition to expand the dissemination of the middleware throughout France and even further, Europe.

BioImageIT overview. a, Schematic view of BioImageIT architecture. The BioImageIT core is composed of data management and data processing functionalities. Users can access plugins by a script editor, Jupyter or the BioImageIT graphical interface (GUI). Data management functionalities exploit local files, remote files or databases such as OMERO. Data processing can perform computations in remote jobs, containers, or local runners. Image analysis is provided by plugins written in different languages. Developers can implement their own plugins in BioImageIT and design their own Graphical Interface. (b-i) LLSM processing workflow gathered in BioImageIT. Hela cell line expressing CD-M6PR-eGFP were stained with Tubulin TrackerTM Deep Red for Microtubules. b, Due to the geometry of LLS scanning, raw 3D images are skewed. c, g, First, realignment (deskew) of raw stacks is performed using Pycudadecon. d, h, Richardson Lucy deconvolution is performed using Pycudadecon. e, CD-M6PR-eGFP vesicles are tracked using Trackmate(FiJi). f, i, Deconvolved stacks and tracks are rendered using napari.

Prigent, S., Valades-Cruz, C.A., Leconte, L. et al. BioImageIT: Open-source framework for integration of image data management with analysis. Nat Methods (2022).

The ability to communicate effectively with each other is one of the strongest predictors for our chances to get ahead in life. In their latest publication in Science Advances, scientists and engineers from IGF-Montpellier (CNRS, INSERM, Univ. Montpellier), IPAM platform (BioCampus Montpellier, France-Bioimaging Montpellier Node) and ARO-Israel demonstrated that this also holds true for GnRH neurons.

In humans and all vertebrates, species survival depends on a critical step during embryonic development: the migration of a small subset of GnRH neurons (about 2,000 in humans and less than 100 in fish) from the nose to the brain where they join the hypothalamus to control reproduction. Their latest results unveiled that GnRH neurons make a pause at the nose-brain frontier where they function as an inter-hemispheric network that is isolated from the rest of the brain. Only neurons that integrate into the network and are able to communicate with their neighbors will finally cross the barrier and make their way into the brain, towards their hypothalamic destination.

In other words, these GnRH neurons, that are critical for species persistence, face the same challenges like other immigrants: they must learn to communicate effectively if they are to integrate into their new world.

In this study, in vivo 2-photon microscopy was a key tool for:

  • Long term imaging with minimal bleaching and phototoxicity
  • Upright configuration enabling dorsal imaging of the fish in its natural position
  • Long-distance water-immersion objectives allowing imaging of deep tissue structures without sacrificing image quality
  • Fast calcium imaging
  • Imaging of red GECI using the higher wavelengths
  • Precise cell ablation
  • Photoactivation of ChR2 while monitoring Ca in the red channel
A graphical model illustrating the migration of a single GnRH neuron (marked by black border) from the nasal placode into the zebrafish brain.

M. Golan, J. Boulanger-Weill, A. Pinot, P. Fontanaud, A. Faucherre, D. S. Gajbhiye, L. Hollander-Cohen, T. Fiordelisio-Coll, A. O. Martin, P. Mollard, Synaptic communication mediates the assembly of a self-organizing circuit that controls reproduction. Sci. Adv. 7, eabc8475 (2021). doi: 10.1126/sciadv.abc8475

Contact: Patrice Mollard, IGF, Montpellier