ZEISS Axio Observer for Life Science Research

Your open and flexible inverted microscope platform with AI assisted experiment startup

Life sciences research calls for reproducible data from a whole range of samples in a variety of conditions. ZEISS Axio Observer is your stable inverse platform for demanding multimodal imaging of living and fixed specimens, giving you:

  • Ensured flexibility for technologies ranging from widefield to gentle super-resolution imaging

  • Unique guidance through your experiments – from sample placement to selecting the perfect imaging modalities

  • Increased efficiency thanks to a high degree of automation, economic light sources, and highest spectral flexibility



ZEISS Axio Observer - Flexibility

Flexibility for Your Research

ZEISS Axio Observer - Flexibility

Life sciences research is a dynamic environment in which your imaging requirements are always changing. As your needs grow, Axio Observer stays with you step by step. It offers an abundance of interfaces for technologies ranging from widefield transmitted light to convenient 3D sectioning with Apotome 3, and sensitive superresolution imaging with Elyra 7 or LSM 980 and Airyscan 2. Choose the optimal incubation equipment and enjoy easy sample access for precise micromanipulation. A great variety of integrated options makes your Axio Observer both versatile now and entirely future proof.

Guidance for Your Workflows

ZEISS Axio Observer - Guidance
Courtesy of M. Schmidt, Institute of Anatomy, Medical Faculty Carl Gustav Carus, Germany.

You will be amazed how easy imaging becomes when the AI Sample Finder automatically detects the sample carrier, adjusts the focus, and finds your sample region. Even with low-contrast samples, you will quickly obtain an overview image to access relevant regions with just a click. Reduce the time to image from minutes to just seconds and start your experiment right away. Let Smart Setup and the Focus Strategy Wizard guide you through the experimental setup for easy and intuitive selection of the imaging modalities for your applications. Using ZEN Connect, acquired images can be easily combined with electron microscopy data and other modalities.

ZEISS Axio Observer - Guidance
Courtesy of M. Schmidt, Institute of Anatomy, Medical Faculty Carl Gustav Carus, Germany.
ZEISS Axio Observer - Efficiency

Efficiency for Your Experiments

ZEISS Axio Observer - Efficiency

Expect a remarkable increase in efficiency with the automation functions of Axio Observer. Use fast switchable LEDs or go for powerful and economic white-light sources in combination with the fast filter wheel for highest spectral flexibility and speed. Select the ideal camera from the dedicated ZEISS Axiocam portfolio or from third-party suppliers: You will always get the image quality and speed your applications require. With Definite Focus 3, focus drift during complicated experiments is a thing of the past. Whether keeping your sample in focus for long-term imaging or adapting your objective to your sample, it's all automatic with this highly organized system.

Product Features

ZEISS Axio Observer - AI Sample Finder

AI Sample Finder

Automated sample identification for efficient imaging

ZEISS Axio Observer - AI Sample Finder

Microscopes are becoming increasingly automated. For sample placement, however, microscope parts such as the condenser arm often have to be moved manually. Focus adjustment and identification of the relevant areas on the sample carrier require additional manual steps. The AI Sample Finder automates this sequence, eliminating time-consuming manual adjustments and reducing the time to image from minutes to just seconds.

You can access all sample areas directly which allows you starting your experiment faster than ever. The AI Sample Finder greatly improves productivity as you can easily image only those regions containing sample not overlooking potentially important areas.

Learn more about AI Sample Finder

ZEISS Axio Observer - Apotome 3

Apotome 3

Optical sectioning using structured illumination

ZEISS Axio Observer - Apotome 3

Create optical sections of your fluorescent samples –with structured illumination, removal of out-of-focus light becomes simple and efficient, allowing you to fully focus on your research. Apotome 3 recognizes the magnification and moves the appropriate grid into the beampath. The system then calculates your optical section from a number of images with different grid positions. It’s a totally reliable way to remove out-of-focus light, even in thicker specimens. Yet your system remains just as easy to operate as always. You get images with high contrast in the best possible resolution – simply brilliant optical sections.

Learn more about Apotome 3

ZEISS Axio Observer - Definite Focus 3

Definite Focus 3

Keep a sharp eye on your goals

ZEISS Axio Observer - Definite Focus 3

Acquiring time-lapse data from living samples can be tricky. Changing conditions such as room temperature influence the microscope as well as the sample carrier and can cause focus drift. Definite Focus 3 compensates for this drift and keeps your samples in focus. With higher accuracy and precision even your most challenging multi-day, multi-position time-lapse experiments will yield sharp and high contrast images.

Here’s how it works: an infrared LED is projected through a grid onto the bottom of the sample carrier. Any change in the focal position of the sample will be indicated by a change of the grid image on the carrier bottom. An integrated camera monitors the shift while the focus drive of the stand moves to compensate for the drift in real-time. Using ZEN imaging software, simply choose a focus strategy and set up your experiment: all compensation happens automatically in the background, without interfering with your acquisition.

Expand Your Possibilities

As your needs grow, you can always expand your Axio Observer. The flexible platform concept provides numerous defined and well documented interfaces. Upgrade new accessories from a broad portfolio of ZEISS solutions or third party offerings.

ZEISS Axio Observer - Objectives
Choose the right objectives for your application from a broad portfolio of lenses.
ZEISS Axio Observer - Duolink
Use Duolink and ZEN imaging software to perform high speed imaging with two spectrally separated channels simultaneously.
ZEISS Axio Observer - Microscope Cameras
Select a microscope camera with the sensitivity, resolution and imaging speed you need.
ZEISS Axio Observer - 3D Imaging Methods
Expand your system with a range of complementary 3D imaging methods.
ZEISS Axio Observer - Incubation Options
Combine your ZEISS Axio Observer with stable incubation options for long-term live cell imaging.
ZEISS Axio Observer - Colibri 7
Choose from efficient LED light sources for gentle fluorescence imaging.

Discover Preconfigured Widefield Microscope Bundles

Tailored to your applications. Flexibly expandable as needed.

Choose from three attractive configurations specifically tailored to either live cell imaging, optical sectioning, or screening applications. Each bundle includes a perfectly matched selection of hardware and software to ensure an efficient workflow from image acquisition to data processing.

Typical Applications

Application Task ZEISS Axio Observer Function

Label-free live cell cultures

Evaluate and document cell culture status

  • PlasDIC contrast for high-resolution images through plastic vessels
  • Objective lenses with long working distance and correction rings to enhance contrast and resolution 
  • Sample carriers and stages for large cell culture flasks
  • Large field of view imaging (field number: 23 mm)

Transfected live cell cultures

Evaluate and document transfection rate and transfection stability

  • Gentle fluorescence excitation by Colibri 5 and Colibri 7

Label-free fixed and thin tissue slices or small organism

Document and evaluate cell and tissue morphology and growth state

  • Optimized DIC for low magnification,
    high numerical aperture multi-immersion lenses

Reproductive or adherent cells and cell cultures

Mechanical manipulation of cells (e.g. injection of germ cells), injection of dyes and other biologically active substances

  • Phase contrast, improved Hoffmann Modulation contrast (iHMC), DIC contrast
  • Support for micromanipulators from Narishige, Eppendorf and Luigs & Neumann 
  • Heated microscope stages and mounting frames, heating inserts

Living neuronal or muscular cell culture or tissue slices

Observation of fast densitometric, ratiometric and electrical signals

  • Water- and silicon oil immersion lenses
  • Apochromatic and UV-enhanced reflected-light illuminator
  • Double camera adapter Duolink
  • Highspeed filter wheels and shutters
  • Fast multicolor LED illumination with Colibri 5 and Colibri 7
  • High efficiency filter sets
  • Z-Piezo (500 µm) with large travel range

Fixed immunfluorescence labelled tissue or cell culture samples

Identification, quantification and qualification of cell types, cell-, tissue and protein markers in 2D and 3D samples

  • Definite Focus 3
  • Dual filter wheel
  • Apotome 3
  • Piezo stage for high speed, high precision XY positioning
  • Various mounting frames for different sample carriers

Multi-labelled living tissue section, organs, organotypic-, spheriod or cell culture preparations

Long-term observation of physiological and morphological parameters in 2D / 3D

  • Autocorr objective lenses
  • Definite Focus 3
  • Special objectives for incubation
  • Life cell imaging objectives
  • Long distance objectives
  • Water and silicone oil immersion objectives
  • Aqua Stop II
  • Incubation, CO2 and O2 control
  • Camera adapter for large field of view imaging (field number: 23 mm)
  • Colibri 5 and Colibri 7

Microbiomes, bacteria and yeast cultures

Identification and characterisation of cell wall, cell cycle and host-parasite interaction

  • C-Apochromat 100 × / 1.25 W Corr
  • APOCHROMAT 150 × / 1.35 Glyc Corr DIC

ZEISS Axio Observer at Work

Lotus Japonicus Root Infected with Symbiotic Bacteria

University of Freiburg, Germany

Autofluorescence of a Lotus Japonicus root infected with symbiotic bacteria stained with mcherry. Sample courtesy of F. A. Ditengou, University of Freiburg, Germany.

ZEISS Axio Observer - Lotus Japonicus Root
ZEISS Axio Observer - Lotus Japonicus Root - Zoom In

Transgenic Zebrafish Larvae

Leibniz-Institute on Aging – Fritz-Lipmann-Institut e.V. (FLI), Germany

Transgenic zebrafish larvae at 4 days post fertilization staining for: Glial fibrillary acidic protein, acetylated Tubulin, GFP and DNA. Embedded in 1.2 % low melt agarose. Sample courtesy of H. Reuter, Leibniz-Institute on Aging – Fritz-Lipmann-Institut e.V. (FLI), Germany.

Widefield + Apotome 3

HeLa Cell Culture

HeLa cell culture with cytosolic eGFP. Proliferation imaged over 16 hours.


HEK 293 Cells

Long-term time lapse recording of 3 × 3 tiles with 240 s interval. Acquired with Axiocam 506 mono, stabilized by Definite Focus 3 at 10 s interval.


SK8 K18 Mouse Cells

Vimentin stained with Alexa 488 (green), nuclei stained with DAPI (blue).

Cortical Neurons

Leibniz-Institute on Aging – Fritz-Lipmann-Institut e.V. (FLI), Germany.

Cortical neurons stained for DNA, microtubules and microtubule-associated proteins.

SK8 K18 Mouse Cells

Vimentin stained with Alexa 488 (green), nuclei stained with DAPI (blue). Left image without correction of cover slip thickness, right with applied correction.

With incorrect cover slip thickness
With applied autocorrection


ZEISS Axio Observer

Your open and flexible inverted microscope platform with AI assisted experiment startup

pages: 24
file size: 3989 kB

ZEISS Axio Observer Bundle for Live Cell Imaging

Matching the environmental conditions of life

pages: 2
file size: 1539 kB

ZEISS Microscope Bundle for Optical Sectioning

Creating crisp sections of thick samples with ease

pages: 2
file size: 940 kB

ZEISS Microscope Bundle for Screening Applications

Fast acquisition and evaluation of large areas

pages: 2
file size: 1059 kB

Technology Note: Plastic Labware for Optimal Results in Modern Life Science Microscopy

Using ZEISS Axio Observer and ZEISS Celldiscoverer 7

pages: 10
file size: 4920 kB

Axio Observer 3-5-7, Axio Observer 3-5-7 materials

Instruction Manual (English)

pages: 194
file size: 11248 kB

Kính hiển vi ZEISS Axio Observer (Vietnamese Version)

Hệ thống kính hiển vi soi ngược nền tảng mở và linh hoạt với công nghệ AI hỗ trợ thiết lập thí nghiệm

pages: 24
file size: 5920 kB

ZEISS Axio Observer (Turkish Version)

Yapay zeka destekli deney başlatma özelliği ile açık ve esnek ters mikroskop platformunuz

pages: 24
file size: 4066 kB

Autoimmersion Module

Quick Guide (English)

pages: 18
file size: 1046 kB

Combined systems for imaging and laser manipulation

Instruction Manual (English)

pages: 42
file size: 2910 kB

Definite Focus 2

Quick Guide (Multiligual)

pages: 86
file size: 6041 kB

Direct FRAP

Instruction Manual (English)

pages: 62
file size: 2672 kB

Filter wheel (CAN)

Quick Guide (English)

pages: 26
file size: 2639 kB

Laser TIRF 3

Instruction Manual (English)

pages: 110
file size: 6065 kB


Instruction Manual (English, German)

pages: 20
file size: 461 kB


Instruction Manual (English)

pages: 24
file size: 838 kB

ZEISS Duolink

Instruction Manual (English)

pages: 38
file size: 1537 kB

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