Upgrade Info

ZEISS Atlas 5 Array TomographyImage Your Serial Sections Fast and Efficiently - with Nanoresolution

Upgrade Info

Contact: Dr. Ulrich Kohl-Roscher

Date: June 2015

Introduction

With Atlas 5 Array Tomography (Atlas 5 AT) you can image

thousands of serial sections of biological tissue or other

large specimens automatically – even at nanometer reso-

lution. This unique, easy-to-use hardware and software

package for your electron microscope has been specifically

designed for automated imaging necessary in an array

tomography workflow. A workflow guides you effortlessly

through all imaging tasks while its many automated func-

tions let you acquire data easier and faster than before. Use

any kind of optical image to navigate your sample - even a

screen grab or photo from your smartphone.

Availability

Atlas 5 AT is available for:

• EVO series

• SIGMA series

• ULTRA series

• SUPRA series

• Crossbeam series

• MERLIN series

• GeminiSEM

ZEISS Atlas 5 Array Tomography Image Your Serial Sections Fast and Efficiently - with Nanoresolution

Benefits

• Tailormade for biological electron microscopy (EM) array

tomography applications. Image large areas and large

numbers of serial sections in the shortest possible time

• Easy to use

Atlas 5 AT’s workflow reduces the time you spend on

setup and data acquisition of hundreds of sections

• Explore Your Data Intuitively

Zoom seamlessly through your image data from centime-

ter-scale optical imagery down to nanometer scale EM

imagery

• Minimize Setup Effort. Maximize Sample Throughput

Using computer-assisted tools, you can define unlimited

regions of interest with any shape over hundreds and

hundreds of serial sections. Easy to use drawing tools let

you select, clone, trace and edit the exact portion of the

sample

• Intelligent Protocols

Put sophisticated imaging protocols in place to define

your acquisition

• Predefined multi resolution imaging protocols, protocol

management, intelligent parameter selection

• Enhanced, robust autofocus and autostigmation functions

anywhere in the sample, with optimized parameters

• Sequential, multi job lists, with the possibility of resuming

and reacquiring any site you wish, at any time, using the

very same or improved parameters

• Large Area Images with Nanometer Resolution

Reduce Your Time to Result with Automated Nano-Imaging of Large Samples.

2

Upgrade Info

3

Specification

Feature Specification

Image Characteristics Continuously selectable up to 32

k x 32 k. Save image data as 8 or

16 bit TIFF files.

Dwell Time Flexible, from 50 ns to

>100 s (with line averaging).

Continuously selectable for opti-

mized imaging.

Autofocus &

Autostigmation

Independent of FOV, image size

and resolution, user tunable for

sample characteristics.

Configurable to minimize impact

on staining samples.

Exact Regions of

Interest

Any shape, arbitrary polygonal,

elliptical or rectangular regions

adjustable ‘on the fly’.

Direction of scan rotation adjust-

ed to shape of site. Precise con-

trol of scanned area.

Data Acquisition Designed for automated acquisi-

tion of large field of view over-

view images and multi-image

mosaics at multiple sites.

Sequential multi-job lists. Possible

to resume and reacquire any

desired site at any time, using the

very same parameters.

Predefined imaging protocols for

common sample preparations.

Correlative

Approaches

Import of optical images for navi-

gation and overlay, and correla-

tion of LM with EM data. ZEISS

Shuttle & Find correlative holders

are integrated.

Data Review Integrated image review. Efficient

review of acquired data and auto-

mated reacquisition of problem-

atic images.

Mosaic Stitching Per image stitching integrated

image correlation algorithms for

mosaic stitching.

Image Processing Shading correction, radial cor-

rections, contrast inversions,

brightness and contrast adjust-

ments, handling of large image

montages.

Export Functionalities Supported formats: TIFF, JPG,

BMP, CZI, CZI image stacks, MRC

image stacks. Export to browser

based viewer included. Export at

imaging resolution or resample.

Merge mosaics into single images

on export.

Upgrade path

Software SmartSEM5.06 or later

SmartSEM API

A system preventive maintenance performed within the last

12 months is mandatory.

The retrofit must be done by an authorised

ZEISS service engineer. Application training is

recommended. For further information, contact:

microscopy@zeiss.com

Part Ordering no.

Atlas 5 AT-NSE 347823-9073-000

Atlas 5 for MERLIN/GeminiSEM

Hardware

347823-9032-000

Atlas 5 for Crossbeam Hardware 347823-9033-000

Atlas 5 Advanced Toolkit Licence 347823-9034-000

Atlas 5 Array Tomography Licence 347823-9035-000

Atlas 5 3D Licence 347823-9036-000

Atlas 5 NPVE Advanced Licences 347823-9037-000

Carl Zeiss Microscopy GmbH 07745 Jena, Germany microscopy@zeiss.com www.zeiss.com/microscopy

EN_4

3_01

1_04

3| C

Z-06

/201

5 | S

ubje

ct t

o ch

ange

in d

esig

n an

d sc

ope

of d

eliv

ery

and

as a

res

ult

of o

ngoi

ng t

echn

ical

dev

elop

men

t. |

© C

arl Z

eiss

Mic

rosc

opy

Gm

bH