On-demand workflow design for image processing and analysis

Bruker 2P+, Discovery laser (680 to 1340 nm), mouse anesthesy and stabulation. Cleared mouse organs (gut, lymph nodes..) and 2P microscopy

Inflammatory and cardiovascular diseases are complex, multifactorial conditions that affect multiple organs and cellular components. To tackle these intricate biological challenges, we employ and advance multi-modal and multi-scale imaging and flow cytometry pipelines. These pipelines include the entire process from sample preparation, image acquisition to image analysis and quantification. Our workflows are adpated to various tissues, including the heart, kidneys, blood vessels, muscles, liver and adipose tissue. They operate across scales ranging from whole organs to subcellular levels, employing techniques such as widefield imaging, confocal spectral imaging, high-resolution imaging (Airyscan, Opera Phenix), high-content imaging (Axioscan 7), and cytometry-based analysis (spectral, sorting, and analysis).

Volumetric electron microscopy : from sample preparation (chemical fixation), to imaging & data processing
(Key-words: SBF, Array-tomography, µCT, micro-wave, nanotomy)

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)

With the help of the CircuitPhotonics platform we can offer several approaches to imaging living organisms, on brain slices with a TriMscope 1 (LaVision Biotec), in mouse brains with several 2-photon excitation stations (and one with 3-photon excitation) Bruker Ultima 2, Karthala, Zeiss NLO …

With the help of the IBDM Lignt Microscopy Facility we can offer an comprehensive CLEM Pipeline from live fluorescence imaging to EM imaging (in 2D and 3D)

As Volume EM techniques we offer Electron Tomography and Serial Blockface Scanning Electron Microscopy. The targeting of a precise ROI can be achieved by integrating Light Microscopy or X-ray imaging in the pipeline.

We work on mouse models (embryos at different stages, mouse organs, tumor samples) with solvent based clearing methods (iDisco modified, home made protocols depending on the samples).