Hyperspectral imaging methods to study cell states in tissues and tumors
Institut Pasteur, Paris France
The Imaging and Modeling Unit at Institut Pasteur is looking for a highly motivated postdoc to develop
advanced microscopy and image reconstruction techniques in order to characterize cellular states and
trajectories within complex tissues in physiology and disease.
During development, cells with identical genomes undergo state changes that are essential to the
formation of organs and entire organisms. When derailed, cellular state changes can lead to pathologies
including cancer and neurodevelopmental disorders. Characterizing cell states at the molecular level in
complex multicellular tissues requires advanced imaging-based technologies that overcome traditional
limits of spatial and temporal resolution, imaging depth and number of simultaneously imaged molecular
species or colors.
To address this challenge, we aim to develop an imaging method able to record a large number of
molecular species (including proteins and RNAs) simultaneously or quasi-simultaneously in mm- or cmthick samples such as brain organoids. For this purpose, we will develop ‘hyperspectral’ light-sheet
imaging approaches with computational reconstruction methods based on AI (deep learning) and/or
compressed sensing. The envisioned imaging system will be based on a hybrid open-top light sheet
microscope recently implemented in our lab in collaboration with J. Liu (Glaser et al. Nat Meth 2022).
We are now looking for a postdoc to lead the development and validation of this system and its
application to hyperspectral imaging of biological samples in collaboration with partner teams.
Expected profile:
- Physicist, engineer or computational scientist
- Strong motivation to work at the interface of physics/engineering/computer science and biology
- Ability to work both autonomously and in collaboration, excellent team spirit
- Good communication skills, fluency in English
The postdoc will be embedded in the Imaging and Modeling Unit, an interdisciplinary team with longstanding network of collaborations.
This project is part of the national PEPR Cell-ID (Cellular identities and destinies) program, funded by
the French National Research Agency (ANR). Cell-ID brings together a multidisciplinary consortium of
laboratories from biophysics to developmental biology and clinical medicine around a common goal:
understanding how cells acquire and maintain their identity during development and why some deviate
from their normal trajectory to give rise to pathologies such as pediatric brain tumors.
Interested candidates please send a CV, letter of motivation with statement of research interests, and
the contact details of at least 3 references to: mickael.lelek@pasteur.fr and czimmer@pasteur.fr