Microscope Software

Microscope Software

Only with the right microscope software you can unleash all features of your imaging station. Our modular software platforms for light microscopes (widefield microscopy), confocal and electron microscopes (SEM, FIB-SEM) systems are easy to learn. They enable you to acquire, process and analyze images in multiple dimensions and over various timepoints. Non-destructive image handling and file formats developed specially for microscopy are just two benefits that guarantee reproducible results for your experiments.

You will be redirected to the ZEISS portal, your interface for downloading software.

Software for Light Microscopes (Widefield) and Confocal Systems


Digital imaging suite for research applications

ZEN is the single user interface you will see on all light microscopy imaging systems from ZEISS.

ZEN lite

Work with microscope images in CZI file format

Perform image acquisition or fundamental image analysis and processing tasks with this free software.

ZEN core

Software for efficient routine workflows

The most comprehensive suite of imaging, segmentation, analysis, and data connectivity tools for multi-modal microscopy.

ZEN starter

Run ZEN core for free

Try out key features for general image acquisition and image analysis.

ZEN Intellesis

For Image Segmentation in Microscopy

Use the power of Deep Learning to easily segment your images.

ZAPHIRE offline evaluation

Bridging microscopy and metrology

Measurement software for automated metrology at a microscopic scale.

PALM RoboSoftware

For PALM microdissection systems

Powerful and intuitive functions for PALM MicroBeam.

Microscopy Apps

Full control over your experiments and imaging

Experience microscopy with the touch of your fingers.

Free 30-Day Version of arivis Vision4D

Your powerful scientific imaging software

Modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size.

Voucher for one year SMA

Explore ZEN core Software Maintenance Agreements

Receive software updates for one year free of charge and preferred application support and service

Get Your APEER Solution now

Automated software solutions

Our cloud-based platform provides you with automated image analysis and an easy-to-use interface.

Software for Electron and X-ray Microscopes


Your software solution for SEM, FE-SEM and FIB-SEM

Use SmartSEM to fully control all operational parameters.

Atlas 5

Master your multi-scale challenge

Large area imaging and sample-centric correlative workflows for ZEISS SEM and FIB-SEM microscopes.


3D Surface Modelling

Use your SEM to reconstruct the surfaces of your samples in 3 dimensions.


Smart Particle Investigator

Your automated SEM particle analysis and classification solution.

ZEN Intellesis

For Image Segmentation in Microscopy

Use the power of Deep Learning to easily segment your images.

ZEISS Mineralogic

Automated Mineralogy

Phase identification and textural analysis in 2D and 3D using ZEISS SEM, XRM, and microCT systems.

Correlative Microscopy

ZEN Connect for Life Sciences

Connect your multi-modal data

Expand correlative microscopy for research on e.g. neuroscience, cell biology or histology.

ZEN Connect for Materials

Connect your multi-modal data

For research on e.g. energy materials like batteries, oil and carbonate rocks or additive manufactured materials.

Correlative Cryo Workflow

Imaging the near-to-native state

Your solution for TEM lamella preparation and volume imaging under cryogenic conditions.

ZEN Correlative Array Tomography

3D correlative light and electron microscopy

Automatically image hundreds of sections across length scales.

Correlative Particle Analysis

Get greater insight and higher quality

Correlative Particle Analyzer combines your data from both light and electron microscopes.

Atlas 5

Master your multi-scale challenge

Create comprehensive multi-scale, multi-modal images with a sample-centric correlative environment.

ZEISS Solutions Lab

Rapid Application Development

You have just purchased a new microscopy system from ZEISS, or perhaps multiple systems to deliver a suite of correlated data across length scales. The possibilities are endless and you are anxious to get to work. So where do you begin? Let us help by taking you through a couple of simple questions.

ZEISS Solutions Lab

Rapid Application Development for Your Tasks

Let us help by taking you through a couple of simple questions.