Tissue processing and imaging-based spatial transcriptomics postdoc

A collaboration between EMBL Rome, EMBL Hamburg and EMBL Heidelberg has been awarded funding from CZI to link the detailed cellular morphology of a tissue with its repertoire of macromolecules: High Throughput X-ray Tomography to Target Transcriptomics (HiTT2T).
The Light Imaging Facility at EMBL Rome have developed spatial-omics technologies that permit multiplex RNA detection in thin tissue sections. Separately, EMBL Hamburg has recently established HiTT (High Throughput Tomography) – an X-ray imaging workflow which offers a fast and high-throughput approach to 3D structural imaging and virtual histology characterisation of entire tissue samples within minutes. The ability to target the 2D-omics data production based on the 3D X-ray data has the potential to revolutionise our understanding of disease. With this proposal, we will move beyond the current state-of-the-art of the methodologies and go to high throughput volumetric tissue analysis and transcriptomics via the development of HiTT2T – High Throughput Tomography to Targeted Transcriptomics. Using the information obtained via HiTT2T and the power of computational analysis presents the possibility of predicting and/or preventing disease with a greater degree of accuracy in the future.
As part of this project there is an opportunity for a 3 year postdoctoral position at EMBL Rome to develop the spatial transcriptomics aspects of the project. The successful candidate will work closely with the EMBL Hamburg teams to ensure sample preparation is optimised for X-ray imaging and can be further processed for imaging-based transcriptomics. In addition the successful candidate will work closely with the computational team at EMBL Heidelberg in order to ensure that maximum value is extracted from the 3D X-ray data and in particular with the position associated with vacancy notice HD02752.
Your role
The fellow is expected to develop tissue processing methods for imaging-based spatial -omics. This position has a strong focus on wet-lab work and experimental protocol development to improve tissue processing methods for -omics. The fellow will work within the Light Imaging Facility at EMBL Rome.
You have:
– PhD in Biology, Pharmacy, Medicine, Chemistry, Bioengineering or related subjects.
– Knowledge in molecular biology
– Experience in tissue, whole-organ or cell sample preparation methods (from basic to IF, RNA visualization up to clearing techniques and expansion microscopy).
– General knowledge in microscopy and image analysis
– Excellent manual dexterity and organizational skills.
– Pro-active attitude and hands-on approach to problem solving.
– Excellent communication, teamwork and interpersonal skills with highest ethical standards.
– Fluency in written and spoken English.
You may have:
– Knowledge in super-resolution microscopy, fluidics or microscopy automation,
– Knowledge in bioinformatics in particular oligo design for RNA or DNA detection as well as analysis of -omics methods.
– Knowledge on multiplex imaging, spatial transcriptomics or bioinformatic analysis of -omics data would be advantageous.
– Knowledge in computer vision and expertise in a programming language such as Python, R or Matlab
For more information, please contact Alvaro Crevenna alvaro.crevenna@embl.it