CZI Image File Format


Image Format for Microscopes

All Your Valuable Data in One File - Safe and Reproducible

  • Multidimensional images
  • Time lapse
  • Z-stacks
  • Multiposition experiments
  • Virtual slides

All Your Valuable Data in One File

The CZI file format has been developed by ZEISS to specifically meet the requirements of imaging in microscopy. ZEN imaging software saves multidimensional images such as time lapse, Z-stacks, multiposition experiments and virtual slides in this format. CZI combines your imaging data with all relevant meta information into one compact file

A growing number of projects and companies already use and support the CZI format with their applications:

  • OME Bio-Formats / OMERO, Fiji & ImageJ, Python (via python-bioformats or, CellProfiler
  • Icy, KNIME, MATLAB, Visiopharm, Imaris, Da-Cons
  • HS-Analysis, arivis Browser / arivis Vision4D, MicrBrightfeld, Indica Labs, Image Pro, Amira
  • Definiens, microDimensions, Orbit, QuPath, digitallabware, TissueGnostics
Microscope and Image Data
Microscope and Image Data

Microscope and Image Data

In addition to the image, the following metadata are stored within the file:

  • acquisition date, keywords, user comments
  • microscope type and settings
  • laser or illumination intensities
  • dimensions and scale bars
  • used contrasts and objectives
  • fluorescent dyes and filters
  • stage (x,y) and focus (z) positions
  • camera and detector parameters such as exposure values, binning, bit depth, pixel dwell time
  • automatic or user-defined graphic elements and annotations
  • sample barcode information

This package of information is always available which means that your imaging is  always reproducible under identical conditions, even years later. If you need to share these images with your colleagues our  free ZEN lite software  allows them to view and process your imaging in CZI format.

If you would also like to process and analyze your CZI images using other software programs, we will be happy to provide you with the internal CZI file format documentation to allow you to do so.  

Mac OS and Linux - Open Software for Open Research

ZEN software and microscopy imaging workstations by ZEISS are designed to run on 64bit Microsoft Windows platforms. To support you on other operating systems such as Mac OS X or Linux, ZEISS offers documentation for interoperability and in addition established  cooperations with partner projects and companies.

Images created with ZEN software and ZEISS microscopy systems are saved in the  fully documented file format CZI. If you wish to view and process data that has been created in this format on non-Windows plattforms we recommend to visit the project homepages of  ImageJ  and the  ImageJ-based Fiji  software package. Precompiled installation files of these open source imaging programs are available for Mac OS X and a number of Linux distributions, as well as a multitude of plug-ins for analysis and processing. CZI image and meta-data import is supported through the  Bio-Formats plug-in of the Open Microscopy Environment.

Please understand that ZEISS Microscopy cannot provide any kind of user-level assistance for these applications. Instead, ZEISS supports open software projects and communities with  developer-level access,  documentation and SDKs  for selected microscopy products. If you are an interested developer you can register for free to get access to the CZI documentation.

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