Cell & Tissue Imaging

Photonics

The optical microscopy resources are spread on 4 geographical sites (Orsay, BDD, Pasteur, Burg) inside the institute each of them with a dedicated staff, and a Nikon Imaging Center (in the Burg building). The advanced microscopy systems have been used in 2017 by about 300 users for a total of more than 63000 hours of use.

All together the equipment in light microscopy comprises in 2018 more than 40 systems: 7 confocal laser scanning microscopes (2 equipped with femtosecond pulsed laser for multiphoton excitation), 8 confocal spinning-disk systems (some equipped with laser photo-perturbation modules), 8 video-microscopes, 3 3D deconvolution microscopes, 2 TIRF systems (with FRAP or PALM techniques), 2 FLIM systems (TCSPC and phase modulation), 2 high-resolution structured illumination microscopes (OMX and Nikon HR-SIM), 2 optical sectioning Zeiss Apotome systems and several standard widefield microscopes for routine observation or histology.

Several techniques are available, some coming from instrumental developments done on the PICT. An example is the fast double TIRF/PALM (high resolution technique) microscope.

The following figure shows the various applications and techniques available on the PICT.

Imaging technologies for biological applications

 

In order to extract relevant information from data acquired on the microscopes, users have access to powerful computers dedicated for image analysis and treatment on each facility sites. In 2010, a compute server (48 cores, 128 Gb RAM) has been installed in the BDD site. Specialized commercial software (Metamorph, Amira, Huygens, Matlab…) as well as several innovative tools developed by the facility staff are now available to every user (Segmentation,tracking, deconvolution, denoising, colocalisation,…).

Indeed, an important part of the staff activity is the development of image analysis and processing tools. Several ImageJ plugins have been done mainly to provide image quantification tools (object counting in 3D, endosomes and cell tracking, mobile part and background separation in movies,…).

Others are integrated under Metamorph software (denoising, wavelet-based segmentation). This brings new insights in the study of the various biological questions addressed by research teams of the Institute.

Also, each member of the staff has an active role in training users of the facility on microscopes and image processing. Since 2010, the 4 sites members are organizing two sessions of an internal training on basic image processing using ImageJ software, and an advanced training (scripting).

They also actively participate or organize regularly national training programs (CNRS, INSERM…) or courses for university master degrees. In September 2016, all members were involved in the organization of the Summer School Mifobio2016 in Seignosse (global organization, lectures, workshops, round tables).