ZEISS Atlas 5

Master Your Multi-scale Challenge

Create comprehensive multi-scale, multi-modal images with a sample-centric correlative environment using Atlas 5. This solution extends the capacity of your ZEISS SEM, FE-SEM (field emission scanning electron microscope) or FIB-SEM (focused ion beam). Efficiently navigate and correlate 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 comprehensive understanding of your sample. Its modular structure lets you tailor Atlas 5 for your everyday needs in materials or life sciences research.

  • Perform large area imaging with ZEISS SEM, FE-SEM & FIB-SEM
  • Acquire nanoscale EM images easier and faster than ever before
  • Correlate images in multiple dimensions from multiple sources
  • Understand your sample by creating unique workflows
  • Work in a correlative workspace, the GUI that places the sample at the center of your workflow
  • Gain speed and achieve precision in z when running a 3D Tomography with Thin & Fast Tomography and True-Z


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.

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.
Solide oxide electrolysis cell, changes after cycling, 3D tomogram, images & EDS data in 3D, ZEISS FIB-SEM, Atlas Analytics. Sample courtesy of: M. Cantoni, EPFL, CH.

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.

Array Tomography

You will have the following tools for array tomography setup:

  • Easily define imaging sites for all sections with the Clone Tool
  • Detect the shape of the section automatically with the Snap Section tool
  • Manage acquisition sites efficiently and even define sub-sites across sections
  • Compile all images into a 3D volume with the image stack export tool and explore them with the image stack viewer
  • Benefit from 3D Stack alignment & image corrections
Polished petrographic thin section, a Peralkaline granite from Northern Quebec
Polished petrographic thin section, a Peralkaline granite from Northern Quebec

Enhanced Browser-based Viewer Export Module

You will analyze, present and share results and train colleagues and students:

  • Export single or multiple datasets to a format that can be viewed in a regular web browser.
  • Even measurements and annotations are possible. 
  • Create curated slideshows based on the data for presentation purposes and embed additional information like pdf files, images, spectra, movies or audio files. 
  • Let your colleagues, students or peers freely explore the dataset at its best resolution and share the data easily by exchanging flash drives or by hosting it on a server.
  • The user can follow the slideshow or pause at any time to explore the data on their own.
Automated FIB-SEM Nanotomography: Acquire simultaneous multi-resolution datasets using xROI and Key Frames.
Automated FIB-SEM Nanotomography: Acquire simultaneous multi-resolution datasets using xROI and Key Frames. Courtesy of: K. Narayan and S. Subramaniam, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

3D Tomography featuring "Thin & Fast Tomography" and "True-Z"

You will execute tomography in three dimensions:

  • Use the 3D FIB-SEM acquisition engine with automated sample preparation to achieve precise 3D visualizations.
  • Measure and precisely control slice thickness during tomography and gain “True-Z” information to process your data accurately.
  • Ensure an accurate, continuous, homogeneous tomogram of samples sensitive to charging, shrinking or beam damage leveraging the “Thin & Fast Tomography”.
  • Get to high quality data faster using xROIs (Exact regions of interest), Advanced sample tracking, predictive drift correction and auto-tuning.
  • Make use of the image stack viewer with 3D FIB-SEM stack alignment and image stack export including cropping.
3D tomography of a multi-layered metal system, a Canadian coin, studied volume: 40 x 40 x 30 μm³ and the voxel size (20 nm)³, EBSD analysis.
3D tomography of a multi-layered metal system, a Canadian coin, studied volume: 40 x 40 x 30 μm³ and the voxel size (20 nm)³, EBSD analysis.


You will perform analytics in 3D with an integrated module:

  • Add 3D EDS/3D EBSD analytics to your high resolution FIB-SEM tomography acquisition.
  • Specify imaging and mapping conditions independently, including landing energy, dwell time and spatial resolution in 3D.
  • Use the advanced acquisition engine to automatically switch between analysis and imaging conditions during acquisition.
  • Acquire 3D tomography datasets in a static configuration for even more stable 3D EBSD runs without any stage moves.
  • Flexible visualization allows you to simultaneously view SEM images and process elemental maps.
  • Integrate 2D EDS mappings into the workflow on your FE-SEM and automatically acquire multiple regions of interest.
A FIB grayscale rendering of the Lincoln Memorial is patterned into silicon with the FIB beam.
A FIB grayscale rendering of the Lincoln Memorial is patterned into silicon with the FIB beam. An unmodified photograph was used as the data source. Patterning time: 10 min.

NPVE Advanced (Advanced Nanopatterning & Visualization Engine)

You will achieve advanced control over patterning geometry and parameters with NPVE:

  • Benefit form simultaneous beam control with full patterning and imaging support for ion and electron beams.
  • Define operation recipes for smart control of the beam and GIS parameters to ensure consistent milling and deposition.
  • Optimize the design of your experiments with 3D profiles and array builder tools.
  • Save up to 40% milling time by iIncluding Fastmill, a special scanning strategy that allows you to prepare FIB cross-sections faster and more efficient.



3D EDS on a tomogram of lead-free solder using ZEISS Crossbeam

Blood vessels of rat brain, thick section, SEM images, mosaic. Atlas  5 Array Tomography.
Blood vessels of rat brain, thick section, SEM images, mosaic. Atlas 5 Array Tomography.
Medicago, root nodules. SEM images by Atlas 5 Array Tomography. Sample: courtesy of J. Sherrier, J. Caplan, S. Modla, University of Delaware, USA.
Polished petrographic thin section, a Peralkaline granite from Northern Quebec
Polished petrographic thin section, a Peralkaline granite from Northern Quebec. Sample courtesy of: A. Gysi, Colorado School of Mines; US.

EDS and EBSD Investigations of a Multi-layered Metal System

Atlas Image Viewer

Atlas 5

Discover datasets from Materials and Life Science research, semiconductor or archeology and explore them with the Browser Based Viewer of ZEISS Atlas 5.

Please click here for the Atlas Image Viewer



ZEISS Atlas 5

Your Solution for Automated Image Acquisition, Data Correlation and Multi-modal 2D & 3D Workflows

pages: 2
file size: 507 kB

ZEISS Atlas 5 Array Tomography

Image Your Serial Sections Fast and Efficiently – with Nanoresolution

pages: 13
file size: 4288 kB

Application Note

Visualization of gold and uranium ore-formation in the Witwatersrand ore deposit from the micro- to nanoscale

pages: 6
file size: 3166 kB

White Paper: ZEISS Atlas 5

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

pages: 7
file size: 1441 kB

White Paper: ZEISS Atlas 5

Large Area Imaging with High Throughput

pages: 6
file size: 4056 kB

Aplication Note: ZEISS Correlative Microscopy

Investigating Structure-property Relationships in a Carbon-fiber Composite

pages: 8
file size: 3204 kB

Application Note:

Cathodoluminescence of Geological Samples: Fluorite Veins

pages: 5
file size: 5476 kB

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

Correlative X-ray and FIB-SEM Microscopy

pages: 6
file size: 1429 kB

Application Note: Multi-scale Correlative Study

Gain insights into corrosion evolution in a magnesium alloy using Atlas 5 that efficiently links and navigates between in situ sub-micron X-ray microscopy, nanoscale X-ray microscopy and FIB-SEM tomography

pages: 8
file size: 1766 kB

Correlative XRM-FIB/SEM

Study of Thermoelectric Materials

pages: 4
file size: 1067 kB

ZEISS Microscopy Solutions for Oil & Gas

Understanding reservoir behavior with pore scale analysis

pages: 13
file size: 4586 kB

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