On-demand workflow design for image processing and analysis

Support for the design and implementation of a cytometry experiment
(Keywords : panel design, sample preparation, data acquisition, data sorting and analysis)

In vivo visualization of plant tissues cellular development, as well as of their response to climate variations
(Key-words : PICPLANT facility with greenhouses (S2), 3 growth chambers for small and large plants, CONVIRON climatic chamber, histology, stereomicroscope, Spectral-FLIM confocal microscope.

Live Imaging and molecular dynamics for cell, organoids, tissue and embryo : from sample preparation with access to a L2 cell culture room, to microscopy and data analysis
(Key words : spinning disk, lattice light sheet, widefield, LightSheet, FRAP, photoconversion, FCS, spot variation FCS, TIRF, single molecule, FRET, FLIM))

Histology : from sample preparation with the RHEM and PHIV facility (human, animal and plant tissue) to digitisation of virtual slides and image analysis
(Key words : brightfield and multiplex staining, Nanozoomer (brightfield), Axioscan (fluorescence), Pannoramic (brightfield and fluorescence), QuPath and Histometrix with machine/deep learning)

Super-resolution-based imaging for cell, tissue and embryo : from sample preparation, to imaging & data processing
(Key-words: Airyscan, STED, STORM, PALM, expansion microscopy alone or combined with other super-resolution technics, data analysis)

Hight-throughput and high content screening : from sample preparation, automation in sample preparation, data acquisition (plate reader or microscopy), image analysis and statistics analysis (list of hits)
(Key-words: chemical libraries, siRNA libraries, sgRNA CRISPR-Cas9 arrayed libraries covering entire genomes (human and mouse), automatic platform for sample preparation, HCS microscopes with low and high resolution, flow cytometer with images)

Mono and bi-photon longitudinal imaging with flexible windows and/or stabilizing chambers for imaging peripheral organs (e.g. heart, lung, liver, gut, pancreas) and human organoids/spheroids/tumoroids implanted in mouse or zebrafish models. This provides information about how they get connected to the blood vasculature.

Longitudinal imaging with one/two colour miniscope with high speed acquisition. Pre-implantation of mouse models with GRIN lenses (objectives from 4 to 7.6mm long and 0.6 to 1.4mm diameter) in brain region expressing specific fluorescent reporters. Mice are imaged for days to several months and fluorescent signals can be correlated with cognitive, behaviour and physiological outcomes.

Intravital mono or bi-photon imaging with either short or long (up to 2 cm) working-distance objectives and coupled with cellular manipulation (mouse, fish and insect models). This can be applied to high resolution cellular imaging of molecule extravasation (e.g. nanobodies, drugs, hormones), capillary blood flow, cellular migration and signaling (e.g. calcium, ligand sensors), and molecule distribution into the extracellular space.

On-demand workflow design for image processing and analysis
(Key-words: Python, Java, ImageJ, Fiji, plugin, macro, notebook, deep-learning)