Frequently Asked Questions

Frequently Asked Questions on ZEISS Imaging Software ZEN and AxioVision

Important Information Regarding the log4shell Vulnerability

AxioVision related Questions

About Image Analysis and Digital Microscopy

  • How do I install AxioVision?
    Find out, which are the minimum and recommended hardware requirements.
    Get information about additional requirements for specific AxioVision Modules included.
  • How do I upgrade my AxioVision PC’s Operating System from 32 to 64-bit?
    This guide goes over the process of upgrading a 32bit AxioVision system to 64-bit Windows, including hardware restrictions and necessary upgrade part numbers.
    AxioVision_Upgrading (status: 10-2014)
  • What's the concept of Scalings? How to create and use them with AxioVision 4.X.X.
    Get an impression: what are Scalings and what are they needed for?
    This guide covers how to create and use both manual and automatic Scalings.
  • How do I calibrate ApoTome?
    Calibrating the ApoTome (for older AxioVision Rel. 4.2)
    Phase Calibration – Grid Focus Calibration – Image Capture using the ApoTome

  • How do I solve problems when installing AxioVision on a non-Zeiss PC?
    Newer computers not specifically provided by Zeiss sometimes require reconfiguration away from factory settings.
    This guide provides tips for reconfiguration. Avoid the camera sharing resources with other devices.
ZEN related Questions for Confocal and Imaging Systems

ELYRA, Lightsheet Z.1, LSM Family

  • How do I install ZEN?
    Read about how to install ZEN Software with the help of the ZEISS Microscopy Installer.
    ZEISS Microscopy Installer
    Software Manual (English)
    Software Manual (Deutsch)
  • How do I determine my version of ZEN?
    Get a quick direction to the menu that reveals the ZEN version.

  • How do I copy favorites buttons and hardware settings?
    This guide discusses how to copy favorites buttons (locate tab) and the associated hardware settings between Windows accounts.  (applies to ZEN 2011, ZEN 2012 and ZEN 2.)
    watch the video
  • How do I install X-Cite LED's in ZEN 2 Blue?
    X-Cite 120LED, 110LED and 120LED mini
    Follow the steps to configure Excelitas’ new LED fluorescent light sources.

  • How do I use the ZEN Blue Image Analysis Module?
    Go over the Image Analysis module in-depth. Find explanations of all measurement tools and formulas.
    (applies to ZEN 2012 and ZEN 2)
    ZEN-Blue_Image-AnalysisGuide (status: 02-2016)

  • How do I
    - use the Physiology Module?
    - work with MeanROI View (Offline)?
    - set up Physiology Experiments?

    Specify user-defined measurement regions (ROIs) following acquisition of my time lapse experiment and analyze their time-dependent changes in intensity.
    Display the intensity curves in diagrams or export the values in the form of tables.

  • How do I
    - use the Tiles & Positions Module?
    - work with User Interface and Functions
    - Workings with Tiles and Positions

    Configure the acquisition of images that consist of several image fields.
    Define Tile Regions or Positions.
    Set up Focus Surfaces and Sample Carrier Templates.

  • How do I create and use scalings with ZEN 2012?
    Find out the width and height of individual pixels ("picture elements") in your digital microscope image. Z-stack images deliver a third dimension for thickness - so called "voxels".

  • How do I store scanning configurations and shortcuts to settings and share that data with other user accounts?
    Read all about the steps to transfer "good" user settings among Windows accounts for AIM/ZEN users.  (applies to AIM through ZEN 2010)
    Share_Configurations  Between_Users

  • How do I perform colocalization in AIM/ZEN Black?
    Explore the steps to effectively perform Colocalization analysis of LSM images.

  • How do I acquire basic FCS measurements using a dye-in-solution sample?
    Learn how to obtain information about particle mobility, concentration, and interaction at a single-molecule level. (applies to ZEN 2010)
    ZEN2010-LSM780  Basic_FCS_Experiments

  • How to fix the  "ZEN 20xx has stopped working" Error?
    ZEN for LSM uses XML files for writing items in the GUI (Graphical User Interface) and if the ZEN program is prematurely shut down there can potentially be corruptions within any number of these XML files.
    (this does not apply to ZEN Blue)
    ZEN20xx_for_LSM stopped_working
Questions to other Topics

Hard- and Software Related

  • How do I use the Labscope App?
    Explore the Labscope iPad app for wireless microscopes and cameras.
    Labscope Software Manual

  • How do I get the resultant theoretical image scaling?
    Use this excel sheet to enter your system information and calculate related optical information such as field of view and scaling factors.
    Offline_Scaling_Calculator_FOV.xlsx  (status: 12-2015)

  • How to set up Primostar HD and Labscope.
    Read how to configure Primostar HD for demos.

  • How do I install /use camera connectors for ZEISS systems?
    Find in this glossary-type document images and descriptions of common computer hardware utilized on ZEISS systems. It includes camera cables, PCI cards, and internal PC connections including what the preferred slots are in Z820 / Z840 PC's.

  • Which Anti-virus Exclusions and Exceptions do exist?
    Get an overview of files, programs, and folder locations which can be added to the exception list of an antivirus program running on the workstation running ZEISS software. Settings these exceptions will help insure AxioVision or ZEN Blue will run unimpeded.
    Anti-Virus-Exclusion-and-Exceptions  (status: 12-2015)