CZI Image File Format


Image Format for Microscopes

All Your Valuable Data in One File - Safe and Reproducible

  • Multidimensional images
  • Muitimodal and MultiScale
  • Fast and efficient compression options (Zstandard and JpegXR)
  • Open-Source friendly with documented APIs
  • Fully integrated into BioFormats

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 visiting 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 several 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.

  • libCZI - Open Source Cross-Platform C++ library to read and write CZI image documents
  • pylibCZIrw - simple and easy-to-use Python wrapper for libCZI ton read and write CZI image documents
  • ZeissImgLib - Advanced .NET library to read and write CZI image documents in .NET applications

Additional tools for CZI image Data

Open-Source and cross-platform Command-Line Interface (CLI) tool to reduce the size of existing CZI-documents by converting them to ZSTD-compressed CZI documents.

Open-Source and cross-platform GUI for CziCompress.

Open-Source and cross-platform Command-Line Interface CLI application to assess the integrity and structural correctness of a CZI document.

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, CellProfiler, QuPath, Icy, Orbit, ...
  • arivis Pro, arivis AI and Cloud, arivis Hub
  • KNIME, MATLAB, Visiopharm, Imaris, Da-Cons, Halo
  • HS-Analysis, MicrBrightfeld, Indica Labs, Image Pro, Amira
  • Definiens, microDimensions, digitallabware, TissueGnostics
Microscope and Image Data
Microscope and Image Data

Microscope and Image Data

In addition to the image, the following metadata (and much more) 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 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. 

Please contact us in case you plan to use our format or the APIs for commercial applications.

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If you want to have more information on data processing at ZEISS please refer to our data privacy notice.