TEFOR Core Facility

In collaboration with its partners within the TEFOR infrastructure, Tefor Core Facility (TCF) develops methods of 3D phenotyping of transparised and marked samples. With other TEFOR partners and international collaborators, TCF works on archiving strategies of volumetric image data in data bases, especially under digital atlases. These strategies are developed in parallel in zebrafish and drosophila models and coordinated by TCF. It also focuses in creating or adapting solutions of easy-to-use and free of charge visualization of big 3D image data. TCF offers standard full phenotyping services of zebrafish larvas and whole adult brains at the subcellular scale, as well as the adpated service of data treatment. TCF develops automatic strategies of volumetric analysis of several organs by segmentation of the volumes of interest for high content screening projects.

High-resolution 3D imaging of big specimens

  • Applying the CLARITY method, lipid-rich tissues can be imaged up to a depth of 2-3 mm with voxels sizes below 1 µmD.

Automatic volumetric analysis of 3D images

  • In collaboration with one of our industrial partners, TEFOR Core Facility develops an automatic image analysis pipeline for high content screening data.

Screening by biphotonic imaging

  • Rapid screening and phenotyping caracterization by biphotonic imaging linked to a vibratome. VibMic allows 3D digitizasion of a wide variety of specimens (anaimls and plants) by automatically alternating blockface-imaging and subsequent vibratome sectioning.


  • Immersion training at TEFOR infrastructure for the implementation of the various techniques: CLARITY, One-for-All, iDisco

VibMic (biphotonic microscopy linked to a vibratome)

  • Immersion training at TEFOR infrastructure
  • Forecasted external trainings


Co-development of imaging solutions for big specimens (in collaboration with Leica Microsystems, Germany).

VibMic is a combination of upright SP8 multiphoton microscope and a conventional vibratome, which enables data registration of big samples, free of the sample depth constraint. Cutting specimens directly under the microscope gives us the opportunity to do the imaging before the cutting, which prevents the damage or loss of sections and results in significantly better 3D reconstructions than the conventional technique.


Development of new 3D phenotyping processes using fluorescence imaging and adapting the most used transparization techniques (CLARITY, I/3-DISCO, SeeDB, CUBIC) to various tissues : immune system, lymphoid tissues, muscle, gonads, gill.

Zebrafish Atlas

Construction of an atlas of the zebrafish and drosophila brains to achieve digital atlases. The goal is to compare the standardised nervous system anatomy of these model organisms to expression patterns of different brains.

TEFOR Core Facility logoGif-s-Yvette

TEFOR Core Facility logoZebrafish

TEFOR Core Facility logodata not available