Acquisition of a Zeiss Microscope

The Department of International Health, Immunology and Microbiology (ISIM) is part of the Faculty of Health and Medical Sciences at the University of Copenhagen and is physically located at the Panum Institutel. 300 scientific and administrative staff members are employed at the Department. ISIM has a revenue of DKK 179 million of which the majority, 77 per cent, is funding from private partners.

Research at the department ranges from basic to applied research and is contained within the four research areas: Bacteriology, Immunology, Virology and Medical Parasitology (malaria research).

A confocal laser scanning microscope LSM 980 with Airyscan2 detector hardware. It is a replacement for our Zeiss LSM 710 with liniarized scan utilized in quantitative imaging, correlation spectroscopy and image correlation which has been discontinued. The new microscope LSM 980 also gives better signal to noise ration and higher speed.

The features of the AiryScan2 is super resolution microscopy for better resolution in XYZ than conventional confocals - so it is very suitable visualizing bacteria interaction in biofilms in 3D/4D. We can really balance between improved resolution, higher sensitivity and specificity of fluorescent indicators, SNR, higher speed or utilize an extra detector - depending on the projects and/or applications we investigate. So it will used for directand much better visualization and understanding of biofilms on explanted implants, and live cell imaging of inflammatory cells interacting with bacteria.

The objective is to set up a new confocal microscope allowing quantitative and quantification experiments comparable to already existing microscope setup.General characteristics for the microscope setup is a

1:1 hardware match regarding motorization, scanning interface and quantitative software to already existing microscope. Experiments and data from the two microscope systems must be comparable and with same data format.In particular.

Acquisition of images according to a position list provided from both microscope systems hardware setup and same data / software format. Acquisitions enabled by motorized components. Acquisition of large area

images or z-stacks using motorized components. z-stack and enhanced depth of focus functionality. Minimum increment of 10 nanometers. Automatically set the correct increment to satisfy the Nyquist criterion. Extraction of the sharp details from individual images at various focus positions and combination into an image with high depth of field. LED excitation in combination with specific emission filter set matching the current

microscope setup for comparable quantitative experiments.Exchange of objectives in between microscopes setup most be possible, especially specification for super resolution. Super resolution

The system includes a detector that will provide super-resolution based on pixel reassignment detection technology. This must give an isotropic increase in resolution down 90 nm lateral and 350 nm axial. Simultaneously the detector must give an increase in SNR (4-8x). Accelerated joint Richardson–Lucy algorithm based super resolution processing. To obtain better statistical interpretation and additional a-priori

information (noise distribution and non negativity) leading to a sample-dependent resolution. Super-resolution based on pixel reassignment detection technology to be used in connection to multiplex mode of 8Y

parallelization with hardware slit aperture in excitation beam path, expanding the laser beam in y-direction. Giving parallel acquisition of 8 image lines and Read-out of 18 center detectors.

Patents:

EP2090918

EP2317362

EP2825908

EP3447559

Our past 15 years of microscopy is based in Zeiss microscopes and a new supplier would lead to difficulties comparing and expanding on existing data sets.