Multimodal Imaging Center (US43-UMS2016)

Images processing and analysing

Expert in analysis of images ranging from light microscopy, cryo-electronic microscopy or ionic microscopy, we help any user to find the best approaches to data processing and analysis.

These requests are studied either after data acquisition or before acquisition to optimize future experiments. A proposal is then made either to use an already existing solution (ImageJ macro or plugin developed by us or by another lab, other software, etc.), or specific development.

Should you require assitance of further information please contact us by email:

Services offer:


→ Help to automate image processing using macros for ImageJ/FIJI software.

Examples of developped automation:

  • Cell counting
  • Counting of foci in nuclei and/or cytoplasm
  • Tracking protein in time series (microtubule growth, transport, etc.)
  • Evaluation of gene expression in the presence of mutation or a compound (chemical, enzymatic, etc.)
  • Colocalization of proteins
  • Measurement of tumor tissue area on histological sections


→ Coding new plugins for ImageJ under condition of collaboration (specific contract or publication)

Recent examples:

  • FIB-SEM: correction of acquisition artifacts in FIB-SEM and inpainting of plans that cannot be corrected

→ Distribution of several plugins for ImageJ already developed by the platform

→ Training of users in image processing and analysis

The engineers of the platform organize and participate in several training sessions throughout the year. These training courses are organized via the CNRS, the Universities or the microscopy networks.