© Fabrice Chrétien, Shahragim Tajbakhsh, Jean-Marc Panaud
Cellule souche (en jaune) de muscle squelettique partiellement recouverte par la membrane basale, migrant sur une fibre musculaire (en bleu).

Human Histopathology and Animal Models


Within our research laboratory, we investigate cell interactions occurring in a homeostatic condition and during and after an injury at the tissue level in both central nervous system (CNS) and skeletal muscle. CNS is protected by the blood-brain barrier and has a resident inflammatory cell population (microglial cells); therefore this is a tissue of choice for studying acute injury, like sepsis. On the other hand, skeletal muscle shows a striking ability to regenerate efficiently and is easily accessible. We use this tissue as a paradigm for chronic lesions and regeneration. In both situations, we aim to characterize tissue compartments and cell interactions through in vivo and in vitro approaches. In the CNS, we study the early involvement of the neurovascular unit during sepsis. In the skeletal muscle, we explore the role of stem cells and stromal partner cells (endothelial cells, macrophages, fibroblasts) at homeostasia and during regeneration.

Our major findings during the last year are (i) that microglial cells are activated very early in the brain after a peripheral infection and during septic shock, (ii) that muscle stem cells show an extreme ability to survive hypoxic environment, keeping with the existence of an hypoxic niche for satellite cells.

Sans titre
Brain histological imaging during sepsis (green: microglia, red: vessels: purple astrocytes)


We have also Expertise activities in Human & Comparative Pathology. We are promoting the analysis of animal models by assisting and educating in their pathological evaluation and to develop diagnosis, research and education in human pathology. Through a Core facility in histopathology with four histo-technicians, we provide a technical support to other research laboratories. We master quality, flexible routine and innovative techniques, like low-melting point paraffin technique for immunohistochemistry of labile antigens, acrylic resin semi-thin sections, or large sections, on either animal or human samples. In this Centre of Expertise, four histopathologists coming from medical and veterinary education contribute to the choice of morphological approaches, the design of protocols, and perform the evaluation of microscopic slides. We were involved last year in more than 30 scientific collaborations mainly in the field of animal models of infectious diseases. The Centre also receives human cases for diagnosis and ancillary techniques, particularly in mycology and parasitology, and we have weekly interactions with the Centre National de Référence des Mycoses Invasives et Antifongiques (Head: Prof F. Dromer).


Program Projects



Histopathological analysis of animal models

About usOur laboratory offers state-of the art large histotechnological laboratory with a team of specialized histopathologists both from medical and veterinary education. The pathologists of our unit are available for collaborative research. Many projects […]


Cryostat in Safety level 3 facility • LEICA • CM 3050S

This material allows us to perform frozen sections from human or animal samples infected with safety level 3 pathogens.Please contact us if needed: David.Briand@pasteur.fr or 31 54

Automated tissue processor • LEICA • TP 1050

This material is needed for routinely dehydration and pre-embedding of tissue samples in paraffin.We can perform the pre-embedding of your tissue samplesPlease contact us if needed: Patricia.Flamant@pasteur.fr or 31 54

Digital camera • NIKON • DSRi2

High quality bright field microphotographs can taken with this material, which is connected to a NIKON 50i microscope.People from other laboratories can have access to this equipmentPlease contact us if needed: Laurence.Fiette@pasteur.fr or 8661 

Vibratome • LEICA • VT 1200S

Vibrating microtomes (vibratomes) allows to cut tissues without freezing or embedding. 50-100 um sections can be performed to study the tissue morphology in 3D or to preserve enzyme and cell activities within thick slices.Trained […]

Cryostat • LEICA • CM 3050S

This material is needed  to perform frozen sections.  People trained in frozen sectioning  from other laboratories can use this material under our supervision.Please contact us.

Automated slide stainer • MICROM • HMS 740

 This automat provides reproducible automated, high quality standard stainings for paraffin or frozen histological sections. Please contact us if you need to stain histological sections (Hematoxylin-Eosin or special stains)Please contact us if needed: Patricia.Flamant@pasteur.fr or […]

Microtome • LEICA • RM 2245

A microtome is needed to perform paraffin sections.Trained people from other laboratories can have access to this equipment under our supervisionPlease contact us if needed: Patricia.Flamant@pasteur.fr or 31 54b. 

Paraffin embedding station • LEICA • EG 1150

The paraffin embedding station is needed to routinely prepare paraffin blocks.We can perform the embedding of your tissue samplesPlease contact us if needed: Patricia.Flamant@pasteur.fr or 31 54

Slide scanner • ZEISS • Axio Scan.Z1

The Axio Scan allow to digitize histological sections and  create high-quality virtual slides. Both bright field and fluorescent sections can be digitalized. Virtual slides can be then be kept and observed or used for […]



Phone: +33 (1) 40 61 39 12
Email: histo@pasteur.fr

25-28 Rue du Docteur Roux
75015, Paris