Atlas 5

Atlas 5 – Large Area Imaging for SEM, FE-SEM & FIB-SEM and Sample-centric, Correlative Workflows for ZEISS Microscopes

ZEISS Atlas 5

Master Your Multi-scale Challenge

Acquire EM Images Easier than Ever Before.

Correlate Images in Multiple Scales.

Atlas 5 makes your life easier: create comprehensive multi-scale, multi-modal images with a sample-centric correlative environment.

Atlas 5 is your powerful hardware and software package that extends the capacity of your ZEISS scanning electron microscopes (SEM) and ZEISS focused ion beam SEMs (FIB-SEM). Use its efficient navigation and correlation of images from any source, e.g. light- and X-ray microscopes. Take full advantage of high throughput and automated large area imaging. Unique workflows help you to gain a deeper understanding of your sample.

Its modular structure lets you tailor Atlas 5 to your everyday needs in materials or life sciences research.


Easy-to-use, workflow-oriented GUI for automated imaging.

Easy-to-use, workflow-oriented GUI for automated imaging.

Acquire EM Images Easier and Faster than Ever Before

  • Acquire large sets of 2D or 3D nanoscale electron microscope (EM) images for hours or days, without operator supervision.
  • Collect single images over thousands of samples, or cover large areas with mosaics comprised of thousands of adjacent images.
  • Atlas 5 streamlines automatic image acquisition, using advanced preset and customizable protocols to produce consistent and reproducible results.

Correlative Workflows between Crossbeam and X-ray & 3D Visualization

Correlate Images from Multiple Sources

  • Bring together images from multiple sources. The correlative workspace of Atlas 5 makes it easy. Zoom in from the full macroscopic view of your sample down to nanoscale details.
  • Efficiently analyze and correlate images from multiple sources. Atlas 5 is your data hub for images from SEM, FIB-SEM, X-ray, light microscopes and any optical images, e.g. from your digital camera.
  • Build a seamless multi-modal, multi-scale picture of your sample with the sample centric workspace of Atlas 5.
3D visualization of plant tissue

3D visualization of plant tissue. Sample: courtesy of J. Sherrier, J. Caplan and S. Modla, University of Delaware, USA.

Understand Your Sample by Creating Unique Workflows

  • Understand your sample fully, in 2D and 3D with the graphical user interface of Atlas 5.
  • Design a workflow tailored precisely to the complexity of your experiment, no matter whether it’s a simple one-step task or a compound experiment.
  • A sophisticated workflow environment guides you from setup for automated acquisition to post processing and customized exports, and right on through to analysis.


Create Large Mosaic Images

Atlas 5 combines a 16 bit scan generator and dual super-sampling signal acquisition hardware with image processing and control software for your ZEISS electron microscope. Acquire images up to 32 k x 32 k pixels on SEMs and up to 40 k x 50 k on FIB-SEMs, with dwell times from 100 ns to > 100 s, adjustable in 100 ns increments. Save your images with eight or sixteen bits of intensity. 

Benefit from:

  • a reduced number of tiles to acquire and reduced computational complexity
  • reducing stage motion delay and areal fraction of each image “lost” to overlap
  • reduced number of overlap “seams”, leading to less beam damage and degradation of the sample

Acquire Images Easier than Ever Before

  • Define your exact region of interest and scan only the designated areas with predefined imaging protocols. Profit from reproducible results by developing protocols with ideal imaging conditions.
  • Keep images sharp during long acquisition times with the help of advanced auto-focus and auto-stigmation tools.
  • Image your sample whenever and wherever you need: Atlas 5 supports multiple sessions on multiple instruments.
  • Correlate images in Atlas 5’s sample-centric correlative workspace - bring together 2D images and 3D volume data from multiple instruments.
  • Import and align data from light, X-ray, electron and FIB-SEM microscopes to produce a single, consistent picture of your sample.

Correlate with X-ray Microscopy to Target Sub-Surface Sites in Your FIB-SEM

  • Correlate X-ray microscopy volume scans from your ZEISS X-ray microscope with surface features visible in your FIB-SEM.
  • Use the X-ray data to virtually localize sub-surface features in 3D to the precisely targeted FIB sites - even if they are not visible in situ.
  • Then navigate to those regions with confidence using your ZEISS FIB-SEM.


ZEISS Atlas 5 Comes with Multiple Offerings

Get to know ZEISS Atlas 5, its modules, their features and their configurability. Extend the capacity of your ZEISS SEM and FIB-SEM with Atlas 5 as an option. Benefit from advanced capabilities of further modules and learn how they are combined.

Atlas 5 modules require Atlas 5. Optional Analytics Module requires ZEISS Oxford Instruments hardware and software package. The Analytics Module on FIB-SEM requires Atlas 5 3D Tomography.

Atlas 5

What you will get from Atlas 5 is:

  • A workflow oriented high throughput acquisition
  • Fusion of images from multiple instruments, detectors and sessions in one correlative workspace
  • Import of several images possible in different file types: BMP, JPG, TIF, CZI, TXM
  • Flexible layered arrangement of images.
  • Protocol based automated 2D acquisition.
  • Large frame store up to 32k × 32k, 100ns dwell time per pixel, 8bit/16bit, 2 channels.
  • xROI imaging (exact regions of interest).
  • Manual stitching of 2D mosaics.
  • Advanced Image Correction (gradient corrections, radial correction, per channel corrections)
  • Advanced Automatic Stitching,
  • Batch Stitching
  • Export to Movie
  • Export to Browser-Based Viewer for web-enabled collaborative data exchange
  • Optimization of protocols per acquisition
  • Export multi-channel data by channel or as blends
  • Integrated image review in a guided review workflow
  • Efficient review of acquired 2D SEM data and automated reacquisition of problematic  

Array Tomography

You will have the following tools for array tomography setup:

  • Clone Tool for section definition
  • Snap Section tool for automated section definition
  • Site Management functions for efficient sub-site definition across sections
  • Image stack viewer and image stack export options

3D Tomography

You will execute tomography in three dimensions with:

  • 3D FIB-SEM acquisition engine with automated sample preparation
  • exact regions of interest (xROI)
  • (xROI) volume imaging 
  • advanced sample tracking
  • adaptive slice thickness tracking
  • predictive drift correction and auto-tuning
  • Image stack viewer with FIB-SEM stack alignment
  • Cropping and image stack export


Perform analytics in 3D with a module integrated in the software interface you use anyway:

  • Add 3D EDS/3D EBSD analytics to high resolution FIB-SEM tomography acquisition
  • Specify imaging and mapping conditions independently, including landing energy, dwell time and spatial resolution in all three dimensions
  • Use the advanced acquisition engine to automatically switch between analysis and imaging conditions during acquisition
  • Flexible visualization allows you to simultaneously view SEM images and process elemental maps
  • Integrate 2D EDS mappings into the workflow on your FE-SEM
  • select regions of interest (ROI) for 2D EDS mappings and automatically acquire multiple selected ROIs

NPVE Advanced (Advanced Nanopatterning & Visualization Engine)

Achieve advanced control over patterning geometry and parameters with NPVE:

  • simultaneous beam control with full patterning and imaging support for ion and electron beams.
  • operation recipes for smart control of beam and GIS parameters for consistent milling and deposition control over the widest range of conditions.
  • set operations, 3D profiles and array builder tools to optimize design of experiments.
  • include Fastmill, a special scanning strategy that allows you to prepare FIB cross-sections faster and more efficient; save up to 40% milling time.
Atlas Image Viewer



Please click here for the Atlas Image Viewer


ZEISS Atlas 5

Master Your Multi-scale Challenge

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Filesize: 8,741 kB

ZEISS Atlas 5 Array Tomography

Image Your Serial Sections Fast and Efficiently – with Nanoresolution

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White Paper: Correlative XRM-FIB/SEM

Study of Thermoelectric Materials

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White Paper: ZEISS Atlas 5

Large Area Imaging with High Throughput

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White Paper: ZEISS Atlas 5

Characterization of Solid Oxide Electrolysis Cells by Advanced FIB-SEM Tomography

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Application Note: Multi-scale Characterization of Lithium Ion Battery Cathode Material

Correlative X-ray and FIB-SEM Microscopy

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Application Note: Multi-scale Correlative Study

Corrosion Evolution in a Magnesium Alloy

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Aplication Note: ZEISS Correlative Microscopy

Investigating Structure-property Relationships in a Carbon-fiber Composite

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