What is the CZI file format?
Files with the .czi extension contain multidimensional images along with the necessary metadata recorded by a ZEISS microscope. They are produced and used by ZEN imaging software and internally stored in the ZISRAW segmented container format. Introduced in 2011, .czi was developed by Carl Zeiss Microscopy GmbH to meet all the requirements set by advanced and professional microscope users, superseding the older .lsm and .zvi formats.
.czi files can include frame-by-frame multidimensional images, Z stacks, multi-position experiments, or whole-slide virtual scans. The format supports up to ten logical dimensions per pixel set - X, Y, Z, channel, time, scene, phase, illumination, rotation, and mosaic tile - making it well suited for complex fluorescence and brightfield acquisitions.
The file saves the image data and metadata such as:
- Document information: title, subject, keywords, recording date, user information
- Image information: dimensions, pixel type, scale for the X, Y, Z axes, annotations
- Microscope settings: model, objective, reflector, contrasting method, fluorescent dyes and filters, stage positions
- Camera settings: type, exposure values, bit depth, merging
Each image is stored as individually compressed sub-blocks that can use uncompressed, JPEG, JPEG XR, LZW, or Zstd compression; a directory segment indexes all sub-blocks for fast random access. The ZISRAW specification is publicly documented for reading, allowing the development of third-party software that utilizes data saved in .czi files, though the write implementation is covered by a confidential addendum.
The .czi format was created to save all necessary information for microscopic imaging in one file. It is utilized by advanced ZEISS devices as well as a host of specialized software, libraries, and projects for analyzing and processing microscopy data - including OME Bio-Formats / OMERO, QuPath, napari (via aicsimageio), Fiji/ImageJ, MATLAB, and the open-source libCZI library. Sharing .czi files is made possible through the freely available ZEN lite software, which allows other users to view, play back, and process the recorded materials.
Security & safety
RISK: LOWCZI is research imaging data with no executable content, so the file itself is low risk. The real concerns are practical: very large files can exhaust RAM/disk (use viewers that stream tiles, like Bio-Formats/QuPath), and exporting to lossy JPG or a single channel silently discards the multidimensional, 16-bit scientific data - always keep the original CZI. Beware "CZI viewer" download sites; use the official ZEISS ZEN lite or open-source Fiji/QuPath instead.
Format details
in a nutshellPrograms that open CZI files
Windows3 apps
ZEISS ZEN lite
Free Install ZEN lite (free, registration) and open the .czi to view all channels/scenes and metadata exactly as acquired.
Fiji / ImageJ (Bio-Formats)
Open-source File > Open the .czi; Bio-Formats' Import dialog lets you pick series/scenes, split channels and view stacks. Recommended over plain ImageJ.
QuPath
Open-source Open the .czi (uses Bio-Formats); choose which scene to open for whole-slide/multi-scene analysis. 
macOS2 apps
Fiji / ImageJ (Bio-Formats)
Open-source Open the .czi via Bio-Formats to view channels, Z-stacks and time series; export to TIFF/OME-TIFF.
QuPath
Open-source Cross-platform whole-slide viewer/analyzer; opens CZI with Bio-Formats and lets you select scenes. 
Linux2 apps
Fiji / ImageJ (Bio-Formats)
Open-source Open the .czi via Bio-Formats; the standard free route on Linux for multidimensional CZI.
napari (with bioio/aicsimageio)
Open-source pip install napari + a CZI reader plugin (bioio-czi), then drag the .czi in to browse dimensions interactively. Technical details
deep spec| Container format | ZISRAW - typed, length-prefixed segment container comprising a file-header segment, image sub-blocks, a metadata block, optional attachments, and a directory segment |
| Encoding | Binary, little-endian byte order |
| Magic bytes | `ZISRAWFILE` - 10 ASCII bytes at offset 0 in the file header; every internal segment begins with a `ZISRAW…` segment ID (e.g. `ZISRAWSUBBLOCK`, `ZISRAWMETADATA`, `ZISRAWATTACH`, `ZISRAWDIRECTORY`) |
| Per-tile compression | Each sub-block is independently compressed: uncompressed, JPEG, JPEG XR, LZW, or Zstd |
| Supported dimensions | Up to 10 logical dimensions per pixel set: X, Y, Z, channel (C), time (T), scene (S), phase (H), illumination (I), rotation (R), and mosaic/tile (M) |
| Pixel types | Gray8, Gray16, Gray32-float, Bgr24, Bgr48; commonly 8- or 16-bit per channel for multi-channel fluorescence |
| Embedded metadata | Full acquisition XML stored in a dedicated `ZISRAWMETADATA` segment; contains microscope, camera, objective, and stage parameters |
| Random access | `ZISRAWDIRECTORY` segment at the end of the file indexes all sub-blocks by position, enabling efficient tile-level random access without sequential scanning |
| Attachments | Optional `ZISRAWATTACH` segments carry thumbnail image, label image, overview image, and acquisition event log |
| MIME type | `image/czi`; fallback `application/octet-stream` |
| Typical file size | Tens of MB to hundreds of GB - whole-slide mosaics and multi-dimensional time-lapse Z-stacks are very large |
| Platform support | Windows, macOS, and Linux via `libCZI`, OME Bio-Formats, and ZEISS ZEN software |
| Specification status | ZISRAW spec publicly documented for reading (enabling third-party readers); write implementation covered by a confidential addendum, so third-party tools generally read but do not author `.czi` files |
| Predecessor formats | Supersedes ZEISS `.lsm` and `.zvi` microscopy image formats |
| Released | 2011 (with ZEISS ZEN imaging software) |
| Latest version | ZISRAW (CZI) File Format Design Specification Release 1.2.x |
| Open standard | Yes · royalty-free |
| Specification | www.zeiss.com |
CZI conversions
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