Zeiss Celldiscoverer 7 User Manual

Product Information

Version 2.0

ZEISS Celldiscoverer7

Your Automated Platform for Live Cell Imaging

Your Automated Platform for Live Cell Imaging

Animation

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

Often in life sciences research, the data you are after will only be revealed using
multiple runs of experiments and complex equipment. Automation can be the
only way to get there. With Celldiscoverer7, you can combine the easy-to-use
automation of a boxed microscope with the image quality and flexibility of a
classic inverted research microscope. Celldiscoverer7 calibrates itself, then
detects and focuses on your samples while the optics adjust themselves.
Leaving you free to get on with other projects. Whether working with 2D or 3D
cell cultures, tissue sections or small model organisms, you will acquire better
data in shorter times with this reliable automated research platform. What’s
more, you can enhance your Celldiscoverer7 with optical sectioning to get more
information from your three-dimensional samples. It’s your choice whether you
opt for confocal imaging with LSM900 and Airyscan2 or fast GPU deconvolution.

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Simpler. More Intelligent. More Integrated.

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

A Flexible Platform

Celldiscoverer7 is a fully integrated high-end

imaging system. It comes with various incubation

and detection options so you can tailor the system

to your applications. Go for fast, sensitive sCMOS

or EMCCD cameras when performing your most

demanding live cell experiments and rapid

time-lapse recordings. To get better data from

your 3D samples, simply add the optional

LSM900 with Airyscan2 for confocal imaging,

or fast GPU-based deconvolution. Get all these

benefits and more with the in-built flexibility of

Celldiscoverer7.

Top Quality Data from Your Samples

For demanding long-term, time-lapse imaging,

Celldiscoverer7 gives you the advantage of Auto-

immersion and a hardware-based focus that finds

and keeps the focus automatically after detecting

the thickness and optical properties of the sample

carrier. Autocorr objectives then correct spherical

aberrations to deliver crisp contrast and high

resolution every time. Get image quality like

you‘ve never seen before – no need to adjust

manually. Keep your cells happy and they’ll deliver

unbiased data: Celldiscoverer7 provides a range

of integrated incubation options to create just the

right environment. The improved optical design

resolves more details in large fields of view.

Reproducible Results Made Easy

As soon as you start imaging, automatic calibration

routines take over to ensure reproducible results.

Check the current status and follow progress of

your experiments on the touchscreen.

With barcode recognition you can identify your

sample, sample carrier and even the type of

experiment. If you don‘t work with barcodes, an

automatic preview scan will identify the sample

carrier and calibrate it. ZEISS predictive service

offers lasting and optimal instrument performance

for increased system uptime and reliable results.

2,5×

20×

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Your Insight into the Technology Behind It

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

An Easy-to-Use Integrated Microscope

Observing live samples over a number of days or imaging lots of multiwell plates really puts your microscope

through its paces. To get reproducible, unbiased data, you must control environmental conditions such as

light, temperature, CO

etc. That’s why Celldiscoverer7 brings you a unique combination of a stable box,

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darkroom and integrated inverted research microscope with optional incubation. It simplifies your laboratory

setup and makes work more comfortable.

All Celldiscoverer7 components are optimized for hassle-free automated imaging. New users and multi-user

facilities especially will enjoy the in-built automation and usability features when setting up complex

experiments. You’ll systematically avoid accidental hardware changes that might lead to biased data or even

damage your microscope. And Celldiscoverer7 can make you more productive, too: expect better data

in shorter times, with less training and maintenance. What’s more, as your needs grow you can expand

Celldiscoverer7 with confocal technology, external cameras, deconvolution, additional environmental

control – whatever you need for the challenge of live cell observation.

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50 µm

72 h cell growth assay using a waterimmersion objective. HeLa Kyoto cells expressing H2B-mCherry Tubulin eGFP (Neumann et al., Nature 2010 Apr.1.; 464(7289):721-7) imaged every 15 minutes for 72 hours using
Autoimmersion; individual channels of the green (eGFP) and red (mCherry) fluorescence and the phase-gradient-contrast as well as an overlay. Sample courtesy of I. Charapitsa, Chemical Biology Core Facility,
EMBL, Heidelberg, Germany

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Your Insight into the Technology Behind It

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

ZEISS Celldiscoverer7 Recognizes and Adapts Automatically to Your Samples

Live cell imaging requires objectives with high numerical apertures. Those objectives will only deliver high

contrast and sensitivity if their optics can adapt to variations in bottom thickness or to the material of

different sample carriers. With Celldiscoverer7 you’re now free to use Petri dishes, chamber slides, multiwell

plates, plastic or glass, thin or thick vessel bottoms, low skirt or high skirt plates. Automatic sample

recognition detects all relevant vessel features while loading your sample. Then Autocorr adjusts the

correction ring of the objective to compensate for spherical aberrations. Find Focus automatically places

your sample in focus and Definite Focus keeps it there. It’s never been easier to get crisp images with low

phototoxicity from deep inside your sample.

Left image shows spherical aberration due to unadjusted optics.
Right image shows the same structure using an Autocorr objective.
The correction results in increased contrast, resolution and
intensity, providing low phototoxicity. The images show tubulin
in FluoCell prepared slide #1. Sample courtesy of Invitrogen,
Thermo Fisher Scientific Inc.

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Your Insight into the Technology Behind It

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

There Is No Life Without Water …

… and no live cell imaging without water immer-

sion. In life sciences, cell biology or screening

applications, your samples mostly consist of water

and / or will be mounted in aqueous solutions.

Celldiscoverer7 combines an outstanding water

immersion objective with rapid automated immer-

sion supply and removal.

A unique elastic silicon membrane fits perfectly

between the objective and sample chamber.

The silicon membrane simultaneously seals the

sample chamber to avoid unnecessary airflow

while protecting the system from potential liquid

spillage. Just select the water immersion objective

and water is supplied instantly to the front lens.

Within seconds the immersion is building up and

the lens is ready to use. When you switch back

to one of Celldiscoverer7’s dry objectives, the

immersion water is automatically removed.

Until now, automated imaging systems often

struggled as the immersion water quickly evapo-

rated. Celldiscoverer7 solves that problem by

automatically monitoring the immersion and

adding water in regular intervals, as needed.

With Celldiscoverer7 you can perform unbiased

live cell experiments at 37 °C over several days or

carry out extensive scanning processes on multi-

well plates.

By adapting the refractive index of your imaging

system to the samples, you’ll achieve more

efficient light collection and increased sensitivity.

And less phototoxicity significantly increases

viability of even your most challenging living

samples.

Heating element of
sample chamber

Sample

Silicone membrane

Membrane opening
with heated objective front

Water immersion objective

A silicone membrane allows automatic water immersion and seals the sample chamber.

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Your Insight into the Technology Behind It

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

Get in Focus, Then Stay in Focus

Use the hardware-based Find Focus function to

automatically focus your sample and find your

region of interest quickly with just a single click.

This significantly reduces the time to your first

image and minimizes sample illumination.

Then select Definite Focus to maintain the focal

position throughout your experiments, whether

it takes a few seconds or several days.

Or combine both methods with the powerful

content-based autofocus of ZEN imaging soft-

ware. Celldiscoverer7 can automatically create

focus maps for multiple positions in long-term

time-lapse experiments. Simply choose the best

focus strategy for the experiment at hand.

Move to the Edge ...

… but not one step more, thanks to the Adaptive

Lens Guard. High optical performance often

compromises on the possible scanning area.

Celldiscoverer7 with its Adaptive Lens Guard

protects the objective from collisions with your

sample vessel or hardware components, automati-

cally maximizing the available scanning area.

Bottom thickness, skirt height and lateral dimen-

sions are important geometrical features of the

different sample carrier types – especially when

working with multiwell plates. Celldiscoverer7

automatically detects these features and adapts

accordingly. It also calculates the maximal possible

scanning area automatically, depending on the

individual sample carrier, objective and current

focus position in your experiment. The available

scanning area is always indicated on your monitor.

Change your experimental parameters and the

scanning area will adapt automatically, in real

time.

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Your Insight into the Technology Behind It

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

Capitalize on LED-Technology for

Live Cell Imaging

Celldiscoverer7 brings you all the advantages of

LED-technology for efficient illumination with low

phototoxicity, fast switching times and long-term

stability. That’s what delivers gentle imaging,

increased throughput and reproducible results.

The fluorescence excitation unit combines up to

seven LEDs for maximum flexibility in the choice

of dyes – from deep blue to far red. All LEDs are

hardware-triggered for precise, fast illumination.

During sample navigation LEDs are tightly synchro-

nized with camera frame rates. An automated

rectangular excitation field stop illuminates only

the active field of view, greatly reducing photo-

toxicity and fluorescence bleaching. Use high-

efficiency multi-bandpass filter sets for fast

acquisition of multiple fluorescent channels.

Celldiscoverer7 simply switches LEDs on / off –

without moving any mechanical parts – so you

get high-speed multi-channel imaging, even when

combined with transmitted light.

SH-SY5Y cells cultured on a 384 microwell plate. Multichannel image at a single position using the 20× / 0.95 objective. Extended depth
of focus from Z-stack. Hoechst – Chromatin (blue), anti-alpha-tubulin antibody FITC for alphas tubulin (green), Phalloidine for actin (red),
MitoTracker Deep Red for mitochondria (purple). Sample courtesy of P. Denner, Core Research Facilities, German Center of Neuro­degenerative Diseases (DZNE), Bonn, Germany.

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› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

Your Insight into the Technology Behind It

100 µm

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Use a Novel Transmitted Light Contrast

With Celldiscoverer7 you can use transmitted

light brightfield and phase gradient contrast.

This novel relief contrast adapts automatically to

the sample carrier geometry, providing excellent

contrast to the very edge of the vessel. It’s fully

compatible with all objectives, filter sets and

sample carriers. This contrasting method stays

robust, even against liquid meniscus or plastic lids.

Use the far-red transmitted light LED for gentle

imaging at very high speeds. You can perform

applications based on label-free assays or let the

system automatically combine transmitted light

with multiple fluorescence channels. All multi-

bandpass filter sets support the combination of

transmitted light and fluorescence, without

reducing sensitivity or speed. On top of that, this

unique motorized transmitted light unit allows

dispensing directly on the optical axis, without

SH-SY5Y cells cultured on a 384 microwell plate. Timelapse
has been acquired using 20× magnification and phase gradient
contrast. Sample and assay courtesy of P. Denner, Core Research
Facilities, German Center of Neurodegenerative Diseases
(DZNE), Bonn, Germany.

disturbing the environmental conditions. The dis-

pensing unit is always integrated. As soon as you

open the hatch on top of your Celldiscoverer7,

the transmitted light unit will automatically

change place with the dispensing unit. You now

have direct on-axis access to the specimen for

pipetting. You can add agents while maintaining

continuous physiological conditions.

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Expand Your Possibilities

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

ZEISS Plan-APOCHROMAT 5× / 0.35

Objective

This objective is your choice for efficient sample

navigation. It creates impressive overview images

by delivering an unparalleled information density

in a single shot, especially in combination with

the microscope camera Axiocam 512 mono.

Many screening applications will strongly benefit

from the high resolution on large fields. The

objective easily handles thin and thick vessel

bottom made of glass or plastic.

In combination with the built-in magnification

changer it combines the benefits of three different

objectives into one: 2.5× / 0.12, 5× / 0.25 and

10× / 0.35 – at a fixed working distance.

ZEISS Plan-APOCHROMAT 20× / 0.7

Autocorr Objective

From thin to thick, from plastic to glass – this

objective adapts automatically to every sample

you load on your Celldiscoverer7. It delivers an

unparalleled numerical aperture of 0.7 through

1.2 mm plastic bottom without compromising

image resolution and contrast. This tremendous

flexibility will make the lens your multipurpose

objective, especially if you would like to image

cells, which can only grow on plastic bottom.

In combination with the built-in magnification

changer this objective combines the benefits of

three different objectives into one: 10× / 0.35, 20× /

0.7 and a 40× / 0.7 – at a fixed working distance.

ZEISS Plan-APOCHROMAT 20× / 0.95

Autocorr Objective

This objective delivers high numerical apertures

without applying immersion. It is optimized for thin

vessel bottoms. No matter if your cells prefer glass

or plastic – this objective will adapt to bottom

material and thickness variations. With the increased

sensitivity this objective is ideal to generate crisp im-

ages on large areas or multiple positions at high

speed. In combination with the built-in magnifica-

tion changer this objective combines the benefits

of three different objectives into one: 10× / 0.5,

20× / 0.8 and 40× / 0.95 – at a fixed working distance.

ZEISS Plan-APOCHROMAT 50× / 1.2 W

Autocorr and Autoimmersion Objective

This objective delivers high light collection effi-

ciency and resolution. In combination with the

Autoimmersion function it matches perfectly to

samples in aqueous solution. Since it reduces

phototoxicity to a minimum, it‘s your choice for

your most demanding life cell imaging applica-

tions, e.g. long-term imaging of subcellular struc-

tures. Optimized for thin bottoms it adapts auto-

ma tically to the bottom material and thickness.

No matter which field of view you prefer, this

objective will deliver a constant numerical aperture

of 1.2 and combines the benefits of three different

objectives into one: 25× / 1.2, 50× / 1.2 and

100× / 1.2 – at a fixed working distance.

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Expand Your Possibilities

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› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

Perform Automated Gentle and

Fast Confocal 3D Imaging

Life happens in 3D – and your research often calls

for optical sectioning to image your samples

with best possible contrast and resolution. Now

you can add LSM900 with Airyscan2 to your

Celldiscoverer7. You get the best of both worlds:

ease of use and automation from a fully integrat-

ed microscope platform and the superb confocal

image quality and flexibility of the LSM9 family

with Airyscan 2. You perform superresolution 3D

imaging with up to 1.5× resolution improvement.

And you easily separate multiple labels with

spectral imaging. You can now analyze dynamic

processes with photomanipulation for FRAP,

FRET or related techniques. It’s never been easier

to precisely connect widefield and confocal

images. Fast mixed-mode acquisition simplifies

and speeds up your workflow and gives you

unique insights into your sample.

The elegant beam path design of your LSM900

with Airyscan2 gives you spectral flexibility.

Each single component is optimized for highest

sensitivity and contrast. Instead of losing light at a

closed pinhole, Airyscan2 collects more emission

light and extracts more spatial information than

classic confocals. You can use Airyscan2 with all

high NA dry or water immersion objectives.

Your live cell imaging benefits from superb image

quality with greatly reduced phototoxicity.

Use low magnification widefield to quickly pre-scan

your complete sample, then identify regions of

interest. It's so easy to then image those regions

with LSM900 and Airyscan2 for optical section-

ing with superresolution. The new Multiplex mode

for Airyscan2 employs smart detection schemes

for this unique area detector. This parallelization

allows to image two times faster, while keeping

best resolution and SNR. Use this mode to image

dynamic processes, or to achieve higher through-

put and productivity.

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› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

Expand Your Possibilities

Rat cortical primary culture. Antibody staining of bIII-tubulin (Cy2,
green), Nestin (Cy3, red) and DCX (Cy5, purple), nuclei stained with
DAPI (blue). 3D reconstruction of the deconvolved Z-stack (shadow
projection). Sample courtesy of H. Braun, LSM Bioanalytik
GmbH, Magdeburg, Germany.

Comparison between widefield (left) and deconvolved (right) Z-stack projection using GPU-based Deconvolution.

Get More Details with Deconvolution

When imaging three-dimensional samples, out-

of-focus light sometimes blurs your structure of

interest. For these images, you need deconvolution –

a combined optical and mathematical method – to

increase contrast and improve the signal-to-noise

ratio and resolution. With Celldiscoverer7 it is

easier than ever before to first acquire a Z-stack

of your samples and then deconvolve the image

to reassign all detected photons to their origin.

With ZEN imaging software you use advanced

deconvolution algorithms, including a novel

approach with depth variant point-spread-func-

tions for deep imaging. Combine this with

Celldiscoverer7’s unique Autocorr objectives

and you will get excellent results from thicker

samples, e.g. 3D-cell culture. And you will get

them up to 30 times faster than with the traditional

technology that works on your processing PC’s

RAM, thanks to Celldiscoverer7’s new GPU-

accelerated, parallel CUDA processing. Use the

increased speed to extract maximum information

from the large datasets you acquired in those

demanding long-term, time-lapse or multiwell

screening applications.

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› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

Expand Your Possibilities

Easily achieve stable environmental conditions

for your demanding live-cell experiments. You can

control the temperature with the optional heating

unit or a Julabo cooling circulator. In combination

with a humidifier, optional CO

you control athmospheric conditions.

and / or O2 module

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Depending on your most common imaging needs,

you can now choose between Axiocam 506 mono

or Axiocam 512 mono.

No matter if you choose a ZEISS Axiocam micro-

scope or a third party camera – if you have to

increase acquisition speed and sensitivity for special

applications, Celldiscoverer’s additional camera

port provides the flexibility you need.

Your Celldiscoverer7 can load multiwell plates,

dishes, chamber-slides or standard slides.

All sample holders are optimized for large scan-

ning areas, fully compatible with water immersion

and autoclavable.

Celldiscoverer7 allows you to run perfusion

experiments efficiently, while maintaining homo-

genous and stable environmental conditions.

Celldiscoverer7 offers an effective way to keep

the sample chamber clean. The insert plate for

UV disinfection is automatically recognized

by the system and you start the disinfection

workflow via the touchscreen.

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Expand Your Possibilities

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

ZEN Imaging Software Shortens the Path

to Your Goal

ZEN – ZEISS Efficient Navigation – is the single

user interface you will see on all imaging systems

from ZEISS. ZEN imaging software leads you

simply and quickly to the result.

At all times you see which options the system

is making available to you and which step is

appropriate to take next. ZEN makes it easy to

operate every imaging system from ZEISS correctly

and intuitively. As a result you save time, reduce

training and support costs, and get faster answers

to your questions.

With Celldiscoverer7 you profit from advanced

automation features:

• Simple and intuitive carrier-based navigation

via mouse and keyboard

• A dedicated automation wizard to create scan

profiles for routine or reoccurring tasks

• A range of hardware- and software-based

focus strategies to set up even complex multi-

position experiments

• Fast overview images. Create an overview of

your cells just once, then there’s no need to

expose them to unnecessary light doses during

experiment setup.

• Cell viability put first with samples illuminated

only as long as the camera acquires an image

• An optimized CZI file format for large datasets

and seamless integration

into existing image analysis workflows

• Open interfaces. Use your CZI dataset in all

major software packages that use the

BioFormats library, e.g., Fiji, Python, Matlab,

Icy, Knime, Imaris, Arivis.

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Expand Your Possibilities

› In Brief

› The Advantages

› The Applications

› The System

› Technology and Details

› Service

OAD is Your Interface

to ZEN Imaging Software

• Use Python scripts to customize and automate

your workflows.

• Integrate external image analysis applications

into your workflows.

• Exchange image data with external programs

like ImageJ, Fiji, MATLAB, KNIME or Python.

• Use feedback for smart experiments.

• Get more reliable data in less time.

It's your choice.

ImageJ

MATLAB

Omero

FIJI

KNIME

OAD enables the analysis of data acquired with ZEN imaging
software by other programs like ImageJ. Transfer your results
back to ZEN for further analysis and display.

Python

The result of overview scan using low magnification (top panel) was used to automatically detect the brain slices via image analysis.
The results (XYZ position and the height / width of detected objects) were used in a automated subsequent scan using a high NA objectives,
where the system carried out an individual tile scan for every detected object in a complete automated fashion without any additional
user interaction. Sample courtesy of P. Grigaravicius, FLI – Leibniz Institute on Aging, Jena, Germany.

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