Scanning Electron Microscopy and X-ray Imaging in Life Science

Microscopy provides an abundance of information about life science specimens. Whether it be live visualization of developmental processes, the capture of ultrastructure at nm resolution or anything in between, the resulting data provides valuable insights into both structure and function of biological specimens.

This webinar series is focused on scanning electron microscopy (SEM) and X-ray imaging. Working at different length-scales and providing complementary information, these two imaging approaches are used both separately and in combination to tackle numerous biological questions.

Each module focuses on a different topic and together these form a solid basis to introduce you to the technologies and application possibilities:

  • Learn how scanning electron microscopy and X-ray imaging work
  • See how you can use these technologies to provide exciting experimental insights in your research
  • Understand the key considerations associated with optimizing your results


Fundamentals of Scanning Electron Microscopy (SEM) in Life Sciences

Aubrey Funke
Product Marketing Manager Life Science Electron Microscopy
ZEISS North America

Scanning Electron Microscopy (SEM) has been long established as a powerful and valuable technique for life science research for samples as varied as insects, tissues, organoids, viruses, cells and plants. Using a beam of electrons to scan the surface of a plethora of sample types, SEM provides a wealth of information about biological structures, high resolution imaging of ultrastructure across large fields of view, compositional information, and the ability to correlate other types of microscopy to link structure and function. Scanning electron microscopes are classically known for imaging structural details on the surface of biological samples but have evolved into providing detailed volume and subcellular information.
Key Learnings:
  • Learn how SEM works and the considerations you need to make when selecting the right imaging parameters
  • See some of the applications that can be addressed using SEM approaches 
  • Hear about some of the challenges that can limit the quality of the images you generate using SEM and how you can avoid them

Watch the session:

Download the associated training guide

Fundamentals of X-ray imaging in Life Sciences

Dr. Rosy Manser
Solution Manager Life Science X-ray Microscopy

Dr. Liz Duke
Team Leader for Biological X-ray Imaging
EMBL Hamburg, Germany

Unlike SEM, imaging with X-rays is non-destructive. X-rays penetrate through specimens and as such are able to capture structural details without physically cutting the sample. Relative to SEM, X-ray imaging is not as well-established in life science research, but the power of the possibilities now offered by instruments based in the lab and at the synchrotron is rapidly changing this balance. The increasing availability of suitable staining and mounting protocols is also aiding the increase in use of X-ray imaging for life science research questions.
Key Learnings:
  • Learn how X-ray tomography works and the numerous instruments that use similar approaches
  • Experience the wide range of applications that can benefit from X-ray imaging, both in the lab at the synchroton
  • Hear about some of the considerations around image quality that come with X-ray imaging and how you can avoid them

Watch the session:

Download the associated training guide

Preparing your Life Science sample for Scanning Electron Microscopy (SEM)

Dr. Kirk Czymmek
Director of the Advanced Bioimaging Laboratory
Donald Danforth Plant Science Center, USA

The very high resolution offered by the SEM comes together with some stringent sample preparation requirements and readying samples for electron microscopy has been known as something of a dark art! Generating the right level of fixation, a smooth embedding and perfect staining takes expertise and practice and many written protocols are not self-explanatory if you don’t have previous experience.
Key Learnings:
  • Learn about the most common sample preparation approaches for SEM in Life Science
  • Hear about some of the common challenges that can limit the quality of the resulting prepared specimen
  • Make yourself familiar with the fundamentals of Volume EM sample preparation

Watch the session:

Download the associated training guides

Expanding your Scanning Electron Microscopy (SEM) to 3-Dimensions and beyond

June 8, 2022 | 4 pm CET | 10 am EDT


Dr. Philipp Bastians
Sales Manager Life Science Electron & X-ray Microscopy
ZEISS North America

The value of SEM in providing high resolution structural information in a wide range of Life Science samples is well appreciated. Developments in technology and sample management capabilities also enable the scaling up of these insights into far larger 2D areas as well as 3D volumes. This expansion of SEM acquisitions provides exciting opportunities for new insights and experiments.
Key Learnings:
  • Learn how you can use different approaches for increasing the area or volume you capture using SEM
  • See some examples of how each of these approaches have expanded the scope of biological questions that can be addressed
  • Hear about the different opportunities that each approach provides
Associated training guide will be available after the presentation
Learn more about structural solutions to benefit your research Select the technology to best suit your needs

Non-destructive Structural Imaging Using X-rays

  • Use state-of-the-art in 3D X-ray microscopy to expand the boundaries of your non-destructive sub-micron scale imaging
  • Benefit from high resolution, even in larger specimens, using two-stage magnification optics and Resolution at a Distance (RaaD)
  • Add the FPX flat panel display for large model imaging
  • Assess internal structure or staining quality of a wide range of specimens without destroying your sample
  • Enjoy high contrast imaging for samples ranging from millimeters to tens of centimeters in size
  • Provide powerful and easy to use microCT imaging that is fully upgradeable to Xradia Versa platforms, so your investment is future proof
  • Enjoy non-destructing X-ray imaging at resolutions down to 50nm
  • Use both absorption and Zernike phase contrast acquisition modes to ensure a diverse range of specimens can be imaged using both stained and unstained sample preparations
  • Study cellular and subcellular structure or particles without the need for complex sample preparation
  • Invest your time and energy into your research rather than costly and time-consuming in-house development
  • Benefit from energy-tunable ultra-high resolution 3D imaging at your synchrotron
  • Achieve fast non-destructive 3D imaging with resolution <30 nm with a variety of contrast modes over a wide energy range from soft to hard X-rays
High Resolution Structural Imaging with Electron Microscopy
  • Capitalize on an entry level, easy to use SEM with both environmental and extended pressure modes to broaden the sample range
  • Accommodate samples up to 30 cm in diameter and optimize imaging conditions for each experiment using the tungsten or lab6 emitter
  • Upgrade your system as your application needs develop
  • Enjoy optimal image quality, even in low contrast samples with the proven Gemini column and beam booster technology
  • Select the optimal detector selection including the on-axis Inlens detector that further drives the efficiency of low kV imaging
  • Enjoy flexible sample management with high vacuum and variable pressure options available
  • Address your most demanding of specimens by providing the highest level of contrast with the proven Gemini column performance
  • Choose from an array of detectors for topography, compositional studies, and autofluorescence as well as additional compatible methods for applications such as exploring nano particles
  • Use the scanning TEM (STEM) detector to provide TEM like imaging to further extend the functionality
  • Scale up your SEM imaging by using up to 91 parallel electron beams
  • Capture cm size regions with nanometer resolution
  • Achieve imaging volume in 4 weeks that would take many years using a FE-SEM
Scaling Your Electron Microscopy to more Dimensions


For High Throughput 3D Analysis and Sample Preparation
  • Visualize 3D structure at the highest resolution across a wide range of sample types and preparations.
  • Image both cryo-preserved and ambient specimens at the highest contrast and best possible image quality with the Gemini column
  • Pinpoint the perfect location by simultaneously milling and viewing your specimen and making dynamic decisions during acquisition

Sense BSD

Your Backscatter Electron Detector for Fast and Gentle Ultrastructural Imaging
  • Well suited for non-conductive, charge-prone biological samples
  • Enables high-contrast imaging with its improved detector sensitivity, even at low kV
  • Produces high-quality images in less time

Atlas 5

Master Your Multi-scale Challenge
  • Provides a smooth workflow solution for Array Tomography
  • 3D Tomography solution
  • Enables and assists with correlative microscopy workflows

ZEN Connect

Overlay and Organize Images from Any Source
  • Overlay and align all your images
  • Acquire overview images for easy navigation
  • Smart data management