Explore thethree-­dimensionalcontext

ZEN 3D Toolkit
Visualization and Analysis of 3D Volume Models

3D Visualization and Rendering
Seeing is BelievingLife Science research has a growing demand for imaging of complex samples. Meaningful­scientific insights are increasingly generated via imaging of whole organisms or organs. Modern
high-content screening experiments make use of 3D models like organoids or spheroids.
ZEISS microscopes from the LSM family, Celldiscoverer 7, Lightsheet 7 or Lattice Lightsheet 7 areespecially designed for 3D imaging with superior optical quality. The ZEN 3D Toolkit package­allows you to efficiently work with the acquired 3D data.

C.elegans dataset acquired with ZEISS Lattice Lightsheet 7. 3D view and orthogonal 2D views facilitated by the Tomo3D viewer.

3D imaging basics: 3D Viewer

Dissecting the sample: Tomo3D Viewer

A dedicated viewer enables high-quality representation ofHaving a nicely rendered 3D visualization is impressive. But

your datasets in 3D. A set of navigation tools, including fly-to rigorously inspect a sample, tools are needed that allow

through methods and zooming and panning, enables intuitive

fast navigation through planes and slices. The Tomo3D viewer

inspection. The viewer is equipped with efficient ray trac-combines a 3D view of the sample with view of arbitrary 2D

ing technology, providing Transparency, Volume, Maximum,

orthogonal clipping planes. These allow you to navigate toSurface, and Mixed methods. It allows adjusting channel

any position of interest while retaining the context of thevisibility, intensity, and opacity. Clipping planes can be intro-

whole sample. Clipping planes allow you to show not only aduced to pronounce regions of special interest and perform

specific section through your sample, but also arbitrary sec-

basic 3D measurements. For visualization and documentation,

tion areas, so you can quickly and insightfully create maxi-

snapshots and movies can be rendered.

mum projection views.

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3D Segmentation and Object Analysis
Quantification is the Proof

Extract information with the Object Table
Read-outs in Life Science imaging can be particularly diverse.
Once object groups have been defined by 3D segmentation,
you might want to access information concerning morphology, object size or numbers, or the distribution and intensity offluorescent signals of any sort. With the Object Table, you canaccess hundreds of measurement parameters. Different object
classes can be accessed separately and sorted by measurement parameters. Arbitrary object subsets can be selected
and highlighted in the 3D viewer.
C.elegans embryo, acquired with ZEISS Lattice Lightsheet 7. Sample courtesy ofExperimental feedback in the 3D space

William Okafornta, Core Facility Cellular Imaging (CFCI), TU Dresden

A very useful and popular ZEN feature is experimental
feedback via Guided Acquisition, which allows pre-selectionMore than nice images: 3D Image Analysis

of sample areas prior to acquisition based on automaticYour scientific work is not limited to examining a sample orimage analysis. With 3D Image Analysis, segmentation iscreating high-quality images for presentations. The ultimate

now e­ xtended to 3D space, where it is especially relevant togoal of any imaging experiment is to obtain meaningful

shorten time-consuming 3D acquisitions.

quantitative data. The 3D Toolkit provides powerful tools
for segmenting 3D objects, working within the established

Crack the tough nuts with arivis Vision4D

workflow of the Image Analysis Wizard. This comes with theThe ZEN 3D Toolkit enables convenient work with 3D data­

convenience of many built-in processing functions that furthersets. For more complex image analysis, your data sets can be

optimize the segmentation, e.g., watershed functions.

easily transferred to arivis Vision4D. Via a data bridge, theThe 3D Toolkit allows you to work with arbitrarily complex

advanced analysis tools of arivis Vision4D are directly acces-class d­ efinitions and derive parent-child relationships. It alsosible from ZEN. Data integrity is ensured by full compatibility

operates with 3D previews.

with the .czi file format.

Intestinal organoid acquired with ZEISS Celldiscoverer 7 and analyzed with the ZEN 3D Toolkit. Two separate types of segmented cell nuclei (orange, green) are
shown within the organoid lumen (magenta).

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Facilitate Your 3D Applications
Efficient Ray Tracing Technology, Even for Large Data

Tomo3D Viewer
3D tomography

3D Image Analysis
3D segmentation and data analysis

Visualize up to six channels and time series data

Define orthogonal 2D views

3D segmentation using the Image Analysis Wizard

Choose from five render modes and work with­clipping planes

Display maximum intensity projections using cut lines

Flexible object representation using different­transparency modes

Rotation, zooming, panning

Adapt the view to your needs by changing the­number and position of the 3D and 2D views

Sort and highlight objects

Create render series and export images(choose your resolution)

Export .csv data

Measure lines and angles
Bridge to arivis vision4D

Requirements• ZEN (blue edition) 3.5• Windows 10, 64 Bit Systems• 64 GB RAM + 8 GB GPU (recommended)

This image and title image: C.elegans embryo, acquired with ZEISS Lattice Lightsheet 7. Sample courtesy of William­Okafornta, Core Facility Cellular Imaging (CFCI), TU Dresden

Carl Zeiss Microscopy GmbH07745 Jena, Germany
microscopy@zeiss.com
www.zeiss.com/microscopy

EN_41_012_276 | CZ 07-2022 | Design, scope of delivery and technical progress subject to change without notice. | © Carl Zeiss Microscopy GmbH

3D Viewer
Basic 3D visualization and rendering

Not for therapeutic use, treatment or medical diagnostic evidence. Not all products are available in every country. Contact your local ZEISS representative for more information.

ZEN 3D Toolkit