

Imaging mouse brains using Light-Sheet Microscopy
arivis Vision4D as prerequisite for stitching and visualizing the mouse brain
- After import, individual z-stacks were aligned and stitched using the Tile Sorter
- Resulting mosaics were visualized in 3D using the 4D viewer
- Movies were generated using the storyboard feature
Handling large data sets to understand interneuron heterogeneity
This study benefitted from arivis Vision4D as the only software with the ability to easily stitch, visualize and share large data sets. Therefore, only the combination of Light-Sheet Microcopy and arivis Vision4D allowed the researchers to obtain 3D information of the entire brain and share this via movies in a very demonstrative way. Based on this, a classical tangential migratory route of CCK interneurons while populating the cerebral cortex was ob-served. Overall, this study identified several characteristics of prenatal CCK interneurons and integrates important information for unravelling the diversity of interneuron functionality
http://cbr.meduniwien.ac.at/ people/persons-details/id/301
https://academic.oup.com/ cercor/article/27/4/2453/ 3056356/Functional- Differentiation-of-Cholecystokinin
Fig 1: Stitching of individual tiles using the Tile Sorter; shown are 35 individual z-stacks covering a dual labelled mouse brain (CCKBAC/DsRed::GAD67gfp/+) at embryonic day 16.5; GA-BAergic neurons are marked by GFP (green) due to expression of GAD67; CCK expression is marked by DsRed (red). Tile 4 is selected and highlighted by a white box. For aligning, the Tile sorter provides different methods including Grid, Manual and Alignments using advanced algorithms. In this case, the z-stack tiles were sorted using the Grid mode; Pixel overlap was set to 10% as during imaging. Several planes were checked to assure correct alignment. Due to stability during image acquisition no further adjustments as algorith-ms were used. Scale options and transparency settings (see selected Tile 4) help to assure correct alignment.
arivis Big data imaging solutions
rivis AG, headquartered in Munich, Germany, is a market leading software company focused on the life sciences industry. arivis AG provides imaging solutions in multi-dimensional microscopy for datasets of basical-ly unlimited file size based on the in-house developed ImageCore technology. With our desktop software arivis Vision4D, scientists are empowered to work with terabyte sized images fast and efficiently on ordinary workstations and laptops. Additional benefit to usability and performance is the possibility to apply color mapping,rendering methods or quantification intuitively with imme-diate feedback and preview of the corresponding results. This potential can be scaled up with arivis WebView, a server-based image analysis framework that allows to access, display and analyze large image data in a standard web browser. With the world’s first and only virtual reality visualization system for real microscopy images, arivis * VisionVR allows scientists to gain all- dimensional insights by fully immersing into the data. www.arivis.com/imaging-science
Source Data set specifications
Microscope: Lightsheet Z.1 microscope (Zeiss), ×5 (EC Plan Neofluar 5×/0.16) detection objective, ×5/0.1 illumination optics, PCO edge sCMOS camera; Imaging settings: ×0.7 zoom, laser power of 20v%, exposure times of 200 ms, tile scan overlap 10%; Data size: 100-300 GB; Picture size: up to 48 tiles, each 1200 px x 1200 px; Voxel size: 1,3 µm x 1,3 µm x 3,5 µm; z-depth: up to 1500 planes
arivis Software Package
arivis Vision4D Base Package