Imaging Solutions for Your Life Science Core Facility
Core Imaging Facilities

Imaging Solutions for Your Life Science Core Facility

Equip Your Facility with the Technology That Enables Your Research Community

The breadth of equipment available in your imaging facility is key in defining the impact, success and growth of your core lab. Providing the right range of solutions ensures your userbase is large and varied and that instrument usage is high so that your return on investment is achieved quickly. ZEISS’ cutting-edge portfolio of tools will set your core facility apart and provide the flexibility and reliability that you need to maintain and expand your userbase.

Find below a selection of trending applications and technologies we have found to be in increasingly high demand in our partner core facilities across the globe.

Live Sample Imaging

Minimizing light interaction with your live specimens is essential for minimizing phototoxic damage and allows longer imaging with more timepoints. Image generated using AICS-0013 (laminB1-mEGFP) from the Allen Institute, Seattle, USA using ZEISS Lattice Lightsheet 7

Capturing Events in Living Specimens

The capacity to image live samples has revolutionized our understanding of modern biology. Developments in technology and sample management continue to expand the range of experiment possibilities. Technology developments are especially important for live imaging since the trade-offs between resolution, speed and sensitivity need to be balanced very carefully. The growing demand for capturing events in living specimens has made live imaging technology a cornerstone of light microscopy core facilities.

Super-Resolution Imaging

Super-Resolution Imaging

Lattice SIM² multi-color imaging at resolution down to 60 nm for conventionally stained samples:
Threefold labeled synaptonemal complexes from mouse testis visualized via immunolabeling of SYCP3 with SeTau647, SYCP1-C with Alexa 488 and SYCP1-N with Alexa 568.

Exploring Specimens at Higher Resolution

Rapid developments in super-resolution technologies, instruments which can resolve details from 20 nm ~ 120 nm, have significantly expanded the range of applications and sample types that can benefit from these techniques. Sample preparation requirements have also become less stringent so more and more specimens can be explored. Many users of fluorescence microscopy are now interested in exploring their specimens at higher resolution and this is driving the need for super-resolution technologies in core imaging labs.

Automated Imaging

Automated Imaging

384 microwell plate, different magnifications in 3 channels, imaged with ZEISS Celldiscoverer 7.
Sample courtesy of P. Denner, Core Research Facilities, German Center of Neurodegenerative Diseases (DZNE), Bonn, Germany.

Increasing Efficiency and Reproducibility

The drive for reproducibility and statistical robustness has fueled an increase in automated and efficient microscopy to both reduce user bias and quickly increase the number of sample points for statistical analysis. Automated imaging can provide the capacity for high content screening, scanning many hundreds of slides, capturing multiplex data, acquiring extended time lapse movies or easy remote operation of imaging equipment. For core imaging facilities these powerful capabilities come with the added benefit of reduced training requirements so users can quickly become self-sufficient.

Cleared Tissue Imaging

Mouse brain cleared using CLARITY protocol with final imaging done in EasyIndex. Acquired with ZEISS Lightsheet 7, processed with ZEN imaging software and arivis Vision4D.
Sample courtesy of E. Diel, D. Richardson. Harvard University, Cambridge, USA.

Imaging Deeper

For large and dense specimens, including brain and large model organisms, tissue clearing is a powerful means to image much deeper without the need for physical sectioning. While some facilities opt for a dedicated cleared tissue imaging system, others may choose a more versatile approach to address the needs of a wider userbase.

High-Resolution Structural Imaging

SARS-CoV-2 grown in a tissue culture and inactivated by chemical fixation

SARS-CoV-2 grown in a tissue culture and inactivated by chemical fixation, negatively stained. Imaged with GeminiSEM 560 scanning transmission electron microscopy.
Sample: courtesy of M. Hannah, Public Health England, United Kingdom.

Revealing the Ultrastructure

Exploring samples using electrons provides a wealth of structural information. The resulting information can be used alone, or in combination with microscopy data from other technologies to uncover details of how structure and function relate to each other.

Users may want to capture structural information in a single 2D image or expand to 3D to look at structure in a complete volume. Core facilities are facing increasing demands to provide solutions that range from imaging water-based samples to vitrified cells to large scale tissue blocks and volumetric acquisitions of resin embedded specimens. Whatever the application the core facility needs to provide solutions that are sufficiently robust and easy to use for a wide userbase to benefit.

Non-Destructive X-ray Imaging

Unstained mouse embryo
Unstained mouse embryo

Unstained mouse embryo (mounted sample) with internal organs highlighted imaged using ZEISS Xradia Versa X-ray microscope. Voxel size: 10.5 µm.
Courtesy of Massachusetts General Hospital, USA

Unstained mouse embryo (mounted sample) with internal organs highlighted imaged using ZEISS Xradia Versa X-ray microscope. Voxel size: 10.5 µm.
Courtesy of Massachusetts General Hospital, USA

Gaining Structural Insights

The non-destructive capture of 3D data using X-rays provides a valuable means of assessing the structure of biological specimens. ZEISS X-ray imaging systems provide both the high-contrast and high-resolution capabilities necessary for clear visualization of internal structures. Core facilities use X-ray imaging for a variety of applications including gaining structural insight from a wide range of specimens, checking sample preparation and integrity before further analysis, such as at the synchrotron, or identifying regions of interest for subsequent exploration using electron microscopy.

Cryo Microscopy

Correlative LM and EM Cryo dataset – from grid overview to the region of interest identified for further TEM tomography.
Sample courtesy of M. Pilhofer, ETH Zürich, Switzerland

Imaging the Near-to-Native State

Native morphology of biological specimens can only be observed when you freeze your sample instead of using chemical fixatives. ZEISS’ field emission scanning electron microscopes (FE-SEMs) and focused ion beam scanning electron microscopes (FIB-SEMs) support cryo workflows and can image your delicate life science samples with outstanding performances at low voltages. ZEISS has also developed a seamless Correlative Cryo Workflow which connects widefield, laser scanning confocal and FIB-SEM in a seamless and easy-to-use procedure that is ideal for use in the core imaging facility.

Multi-Modal Imaging

Petri dish overview scan using a widefield microscope
Petri dish overview scan using a widefield microscope

Petri dish overview scan using a widefield microscope. The tiled images are used to align the sample to the next microscope. After transferring the petri dish to the LSM, time series were taken through a complete 4D approach using time and z information to visualize the dynamics of the microtubules.

Petri dish overview scan using a widefield microscope. The tiled images are used to align the sample to the next microscope. After transferring the petri dish to the LSM, time series were taken through a complete 4D approach using time and z information to visualize the dynamics of the microtubules.

Keeping Data in Context

Thorough investigation of biological samples often requires the use of more than one imaging approach. As the leading manufacturer of imaging solutions across the range of length scales, from light to X-ray to electron microscopy, ZEISS has created easy solutions for multi-modal imaging to guide you through all possible workflows. In addition, ZEN software provides a means of not only storing the data from each of the technologies in context, with a record of where each piece of valuable information resides relative to the others, but also offers a means of aligning these data in three dimensions so that valuable insights can be revealed. You can import data from any microscope system into ZEN and results from approaches other than imaging can even be added so your users keep a record of all their data about each sample in one place.


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