• Image Analysis
  • Single Cell / Single Molecule

CartoBrain – High-resolution mapping of neural networks by optical microscopy in preclinical research

Project lead by  Thierry Delzescaux
Industrial partners  Neoxia


The objective of this doctoral work will be to develop original software tools to study neuron populations at the whole-brain scale in preclinical research. The images will be acquired by optical microscopy at very high magnification factor to allow individualization at cellular scale.

Enumeration and modelling of the cytoarchitecture (distribution/organization) will provide new information of great interest in both healthy (anatomy, development) and pathological (neurodegenerative diseases, neuronal death) cases.

Advanced image processing techniques will be used to carry out these analyses (machine learning, high performance computing, massive data processing).

Finally, a validation of the results obtained on multi-species data produced at the CEA MIRCen will be carried out by comparing the results obtained with the reference technique of stereology (cell counting) and anatomical segmentations of reference (expert neuroanatomist, brain digital atlases).

A technological transfer of cell counting software developed during the project will be carried out in close collaboration with Neoxia, a company implementing a cloud-based platform for large biological images processing.



As a response to the : Call for projects 2019 : Paris Region PhD²

Paris Region PhD² : call for applications for the funding of PhD grants

Details & Selected Projects


  • Neurodegenerative Diseases Laboratory

    CEA - French Alternative Energies and Atomic Energy Commission
    François Jacob Institute of biology

    Read more