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Institute of Solid state Electronics

Department of Bioelectronics
Univ. Prof. Dr. H.-U. Dodt 

Vienna University of Technology

Gusshausstr. 29

A-1040 Vienna
Austria

Email: dodt@tuwien.ac.at

Additional Address:

Section of Bioelectronics
Center for Brain Research


Spitalgasse 4
A-1090 Vienna

Areas of Research

We are working on further improvement of the images obtained by ultramicroscopy by different means. These include approaches which further reduce scattered light induced by the illumination of the specimen.

Current Projects (Optics)


Developement of an ultrathin light sheet with long Rayleight Range
We are working on further improvement of the images obtained by ultramicroscopy by different means. These include approaches which further reduce scattered light induced by the illumination of the specimen. Another approach will be the use of adaptive optics to increase visualisation depth. Apart from the optical set-up we found that the clearing procedure is of highest importance. We are therefore exploring new clearing protocols for various specimens. This is especially important for heavily myelinated structures. Neural plasticity We intend to increase the resolution of our technique to reliably identify and count dendritic spines. We will then investigate several experimental paradigms to induce neuronal plasticity. By comparison of control and experimental groups of  mice with GFP labelled neurons, we hope to identify alterations in spine density depending on the experiment.

Developement of refractive matched objectives
Systematic study of flight musculature structure in intact adult Drosophila.  We use flies with genetically knocked-down gene product that leads to flightless flies (in collaboration with Frank Schnorrer, Muscle Dynamics, MPI of Biochemistry, Munich, Germany). By applying ultramicroscopy we are able to analyse the 3D-structure of adult flight muscles in these flightless animals and compare them to wild type.

Converter to transform a multimode laser beam into a single mode beam
Systematic study of flight musculature structure in intact adult Drosophila.  We use flies with genetically knocked-down gene product that leads to flightless flies (in collaboration with Frank Schnorrer, Muscle Dynamics, MPI of Biochemistry, Munich, Germany). By applying ultramicroscopy we are able to analyse the 3D-structure of adult flight muscles in these flightless animals and compare them to wild types.

Current Projects (Imaging)
High resolution recording of mouse brains
Using the ultrathin light sheet we obtain nearly isotropic recordings of mouse brains. With suitable objectives we are able to visualize dendritic spines in both CLARITY and sDISCO cleared brains. This is remarkable as CLARITY cleared brains are about twice as big as sDISCO cleared brains. In an ongoing WWTF project with the MPI of Psychiatry (Dr. Wotjak) we want to see if spine density is correlated with behavioural learning. With the MPI group we also try to visualize learning induced neuronal activity by recording fluorescence in activated neurons after expression of immediate early genes (cfos, Arc). With our elaborated optics we will even try to record activity induced fluorescence in neuronal dendrites in the cleared brains.


3-D Pathology of human tumors
Pathological diagnostics of tumor resectates after cancer surgery is traditionally based on the inspection of 5µm thin mechanical sections. As the removed tumor can be quite large on average only every 5 mm such a histological section is prepared implicating an undersampling factor of 1000. So cancer cells between the mechanical sections may be missed and the final diagnostics can be wrong leading to suboptimal therapy decisions. A new powerful clearing allows us to clear tumor samples the standard size for histological cassettes (2 x 3 x 0.5 cm). By boosted autofluorescence we are able to visualize at lower magnification the overall structure of the tumor and blood vessels and at higher magnification single cells. As this is possible to the whole thickness of the tumor sample we should in principle be able to scan the whole resectate at cellular resolution. This should allow in future much safer pathological diagnostics. In addition the 3D image obtained may provide information about the cancer hitherto not available. Especially the reconstruction of the blood vessel system may give valuable insights into the neovascularization of the tumor which can be important for staging.


Current Projects (Deconvolution)
Presently, there is a lack of suitable free software for deconvolving light sheet microscopy (LSM) recordings obtained with low magnification objectives and large fields of view. Therefore, we are developing a deconvolution software, which allows to deconvolve even very large image stacks (e.g. 20 GB or more) as typically produced by LSM of cleared samples. Since we utilize a theoretical point spread function (PSF), that we derived from an optical model of image generation in a LSM (Becker et al., 2019, Scientiffic Reports, https://doi.org/10.1038/s41598-019-53875-y), no error-prone PSF measurements by recording of fluorescent beads are required. Due to parallel processing on multiple CPUs and utilizing the GPU (graphics processor) for FFT calculation the speed of our software competes with commercial software packages as e.g. Huygens (SVI, Netherlands) or AutoQuant (Media Cybernetics, USA).