arivis Scientific Image Analysis

Tiling and Stitching

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Stitching and Alignment

Various applications require a process named stitching and alignment as a prerequisite step for the visualization of 3D or 4D volumetric files. Here, every plane of the resulting image is combined of a number of tiles acquired separately.
ZEISS arivis Pro (formerly Vision4D) is the unique tool for effective stitching and alignment of hundreds to thousands of multiple single files (tiles), which may create volumes of several hundred gigabyte or even terabyte in total file size.
The arivis Tile Sorter allows for a complete interactive adjustment for stitching.

arivis Vision4D-Tile-Sorter screenshot

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  • Arrange single and isolated image tiles to a large stitched volume
  • Plane shift for tile stacks
  • Supports source data with tiles organized as scopes
  • Support for manually rotated tiles
  • Manual as well as automatic stitching and blending
  • Blending between overlapping regions
  • Methods for aligning
  • Grid: Manually define order & overlap based on equally distributed grid
  • Manual: Drag and drop single tiles by hand
  • Alignment: Advanced algorithms will find and align matching tiles
  • Optional maximum Intensity Projection (MIP) mode to improve results
  • Import, review & stitching of TrakEM2 projects
  • Powerful Alignment algorithms and optimizers
  • Phase Correlation Method (PCM)
  • Normalized Cross Correlation Method (FFT-NCC)
  • Template matching alignment
  • Energy optimizer
  • SVD optimizer

Courtesy of M. Paoli, Galizia Lab, University of Konstanz, Germany, Image acquisition with ZEISS LSM with Airyscan
Image Details: The brain, thoracic and abdominal ganglia of the cockroach are joined together by bilateral connective bundles of ascending and descending interneurons forming the ventral nerve cord. In this preparation, left and right connectives were individually labelled (Alexa 488: green, Alexa 647: magenta) posteriorly to the suboesophageal ganglion to observe the extension of their innervation within the different neurophils, and throughout the ipsi- and contralateral parts of the brain (DNA labelled with DAPI: cyan). Imaging was performed using Tiling and Stitching to capture the complete volume (3×2.3× 0.26 mm). 3D animation of the complete dataset was done with ZEISS arivis Pro (formerly Vision4D), ideal for rendering and analyzing large datasets. The 4D viewer in ZEISS arivis Pro (Vision4D) can be configured to adjust the appearance of individual channels independently to highlight specific features.

The arivis Image Analysis Platform

The arivis Scientific Image Analysis Platform is a flexible computing universe that scales, parallelizes, and streamlines all imaging workflows. With arivis' easy sharing functions your organization can enjoy data proficiency and efficiency at new levels. arivis includes integrated toolsets that handle everything, from file storage format to project and user-specific computations, to reporting. The platform's hubs connect datasets and manage central imaging databases and raw data exposure, while also enabling Machine Learning and AI routines.

placeholder40px ZEISS arivis Hub A nucleus of computational activity and collaboration at scale. ZEISS arivis Hub enables design and execution of large-scale experiments that produce results from images, whether datasets are already stored or are actively being produced. Mass quantities of microscopy data are onboarded and processed by a virtual team of computational workers. Smartly utilize processing cores in servers or workstations with maximum possible speed.  
placeholder40px ZEISS arivis Pro

Extract results from your scientific images with ZEISS arivis Pro. Make the most of hardware power adjustments and smooth interactivity on microscopy datasets of virtually unlimited size. The software unites multiple tools for visualization and advanced analysis into one easy-to-learn user environment for high productivity. Extend your possibilities with the Python coding feature and a multitude of supported libraries and APIs. Optional Virtual Reality interface.

placeholder40px ZEISS arivis Cloud Train Deep Learning models to automate your image analysis in ZEISS arivis Cloud (formerly APEER). Whether you use standard pipelines for routine tasks or create your own application, you can power your research with AI with just a few clicks. You can train your own model or alternatively, select a pre-defined pipeline and use a previously trained model on your images. The AI-trained models can be used with other ZEISS software products. Read More

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