Visualization of Large 3D Tissue Samples (ViLTiS)
The Zeiss Arivis Vision 4D software now provides a variety of tools for creating pipelines for cell and particle tracking in 3D microscopy - the Alliance supported its use on campus.
In April 2023, the DKFZ Light Microscopy Core Facility installed a new Zeiss Lightsheet 7 (LS7) microscope. This initiative paved the way for a collaborative agreement between DKFZ and Heidelberg University, providing all project partners with access to 3D light-sheet microscopy technology.
Several project members were trained in the use of this microscope in August and September 2023. As planned, the funds from project ViLTiS were used to purchase a license for Zeiss Arivis Vision 4D. This modular software includes a variety of tools for creating customized analysis pipelines, as well as a wide range of integrated sample pipelines such as cell and particle tracking. It facilitates the rapid handling and analysis of large data sets, a common feature in 3D microscopy. All project partners were trained in two workshop series.
The following experiments showed that the new software is advantageous for characterizing the density, morphology, and motility of encapsulated cells in large light-sheet microscopy data sets. In addition, several users of the Z7 light-sheet microscope have begun using the Arivis software for specific image processing tasks such as cell segmentation, tracking cell-spheroid infiltration, 3D visualization, neuron tracing, and whole mouse brain stitching and analysis.
Starting in October 2023, the Carl-Zeiss-Foundation has funded Kai Melde to establish a new research group to develop holographic tools for biofabrication. As a consequence, there will be a constant need for imaging and analysis of large tissue samples. The goal of this project is to assemble cells using a holographic acoustic field. The samples are centimeter-sized hydrogel blocks with encapsulated cells.
The group uses light-sheet microscopy at 5x and 20x magnification to study cell micro-patterns, separation and directionality via 3D volumetric imaging (using tiles and z-scanning) at single cell resolution. After image acquisition and post-processing, cell segmentation and feature measurements such as local cell density have been successfully performed using Arivis software.