me

By and large, I collaborate with Life Scientists to help them optimize their imaging experiments for quantitative analysis and tailor image analysis software tools to extract relevant information backing their research hypotheses.

I have a long experience working in facility settings (IRB Barcelona advanced microscopy Core Facility, Danish BioImaging Image Analysis Core Facility) dealing with a wide range of research projects, light microscopy datasets, and common software packages.

I have been especially active in the field of microscope intelligent automation (AUTOSCANJ, Frontiers Bioinformatics 2021), image restoration (MosaicExplorerJ, F1000 Research 2021) and the design of software frameworks (LOBSTER, Bioinformatics 2020, LIA-J, THEIA) for the identification of biological objects in large optically cleared images acquired by custom lightsheet microscopes (including DIY microscope such as the LEMOLISH-mot) towards tissue modelling.

As workgroup leader of the Network of European BioImage Analysts (NEUBIAS COST Action), I contributed to shape a new BioImage Analysis teaching curriculum for Life Scientists, organized numerous international training schools, and helped set good practices for the publication and benchmarking of bioimage analysis tools and protocols (BIAFLOWS, Patterns 2020). I also seeded and temporarily led a pioneer BioImage Analysis Open Core Facility (part of Danish Bioimaging Infrastructure) with a focus on fully remote access and computing infrastructure services.

More recently, I integrated a core cell biology lab (Biophysics in Cell Biology Research Group, University Pompeu Fabra) where I help the group improving imaging experiments (interface to imaging add-on modules, super-resolution, image restoration) and develop software tools to quantitatively track Exocytosis events in yeast cells towards the understanding of the exocyst, partner proteins machinery, and evolutionary adaption to temperature change. I also support other groups from the department in bioimage analysis through the Open OnDemand platform enabling the scalable deployment of reproducible analysis workflows to the department HPC cluster.

Contact sebastien.tosi@gmail.com