CZI conversion

Convert CZI to TIFF or OME-TIFF on Windows and Mac

Convert CZI files to OME-TIFF, the open TIFF that keeps channel names and pixel size, with the vendor's software, with free Fiji or bfconvert, with a few lines of Python, or in SlideScope without code. Prefer OME-TIFF to a plain TIFF: a plain TIFF usually loses the calibration and channel metadata. And keep unpublished data off online converters, which upload your file.

Download SlideScopeAll conversion options
Lossless OME-TIFFChannels and calibration keptNo upload

Ways to convert CZI to TIFF

ToolCostPlatformsNotes
ZEISS ZENPaid; ZEN lite is freeWindows onlyImage Export (TIFF) and OME TIFF Export; tiles are not available for OME TIFF Export
Fiji / ImageJ with Bio-FormatsFree, open sourceWindows, macOS, LinuxBio-Formats Exporter to OME-TIFF; cannot read JPEG-XR CZI on Apple silicon
bfconvert (Bio-Formats tools)Free, open sourceWindows, macOS, LinuxCommand line; batch, BigTIFF, pyramids, compression
Python (bioio, pylibCZIrw)Free, open sourceWindows, macOS, LinuxScripted conversion; needs Python
SlideScopePaid; export comes with the 3-day free trialWindows 10/11, macOS 14+Lossless OME-TIFF with channels and calibration, every scene of a multi-scene CZI, no code, no upload

Online converters are the one option to avoid for research data: they upload the file to someone else’s server, and several cannot read CZI at all (convert.guru, for one, says you need ZEN).

Convert CZI to TIFF in ZEISS ZEN (Windows)

  1. Open the CZI in ZEN and go to the Processing tab.
  2. Under Method, choose Export/Import › OME TIFF Export (or Image Export for plain TIFF, BMP or JPEG).
  3. Set the output folder and options and click Apply. For many files, use Processing › Batch with the Image Export method.

ZEISS notes that tiles are not available for OME TIFF Export. ZEN lite is ZEISS’s free edition; ZEISS does not list its export functions, though a University of Arizona install guide describes using it for export. ZEN runs on Windows only.

Convert CZI to OME-TIFF in Fiji or with bfconvert (free)

  1. In Fiji, open the CZI file (it goes through the Bio-Formats importer).
  2. Choose Plugins › Bio-Formats › Bio-Formats Exporter and save as .ome.tif. For files over 4 GB use a BigTIFF extension such as .ome.btf; a plain .tif is limited to 4 GB.

Without opening Fiji, the Bio-Formats command-line tools convert from a terminal (download bftools.zip from the Bio-Formats site):

bfconvert input.czi output.ome.tiff
bfconvert -bigtiff -compression LZW -tilex 512 -tiley 512 input.czi output.ome.tiff
bfconvert -noflat -pyramid-resolutions 4 -pyramid-scale 2 input.czi output.ome.tiff

The output format follows the extension; output is uncompressed unless you pass -compression; -series 0 converts one series only. The pyramid form needs -noflat, which only OME-TIFF supports.

Convert CZI in Python

bioio reads CZI (with the bioio-czi plugin) and writes OME-TIFF (with bioio-ome-tiff):

from bioio import BioImage

BioImage("input.czi").save("output.ome.tiff")

ZEISS’s own pylibCZIrw reads CZI planes and regions (pyczi.open_czi(path), then read(plane=...)) but does not write TIFF: pair it with tifffile if you need full control over what is written.

Convert CZI to OME-TIFF in SlideScope (no code)

  1. Open the CZI file in SlideScope on Windows or Mac.
  2. Choose File › Export Current Image as TIFF… and pick a destination. SlideScope writes a lossless OME-TIFF (.ome.tif) with the channel names, colours and pixel size, and never changes the original file. A multi-scene CZI viewed one scene at a time exports the scene on screen, at that scene’s own resolution.
  3. For many files, choose File › Open Folder, select the files, and run “Export the selected files…” for one OME-TIFF per file, with each scene or position kept as its own image inside it; “Extract scenes from the selected files…” writes each scene or position as a separate file instead. For large slide scans choose “Full resolution: every scanned pixel”.
  4. Open the result in Fiji, QuPath or any OME-TIFF reader: Fiji hands .ome.tif files to Bio-Formats, which reads the calibration and channels.

Export comes with the 3-day free trial (the free preview opens, measures and annotates up to 5 images). The conversion runs on your own computer; nothing is uploaded.

CZI conversion questions

Can I convert CZI to TIFF for free?

Yes. Fiji (free) opens CZI through Bio-Formats and saves OME-TIFF with Plugins › Bio-Formats › Bio-Formats Exporter, and the free bfconvert command does the same from a terminal. On a Windows PC, ZEISS ZEN also exports CZI to TIFF and OME-TIFF.

Should I export TIFF or OME-TIFF?

OME-TIFF. It is still a TIFF that most programs open, but it keeps the channel names, the pixel size and the Z and time structure in its metadata. A plain TIFF usually keeps only the pixels, so measurements in other software come out in pixels instead of µm.

Why does my exported TIFF look black or very dark?

Most microscope images are 12- or 16-bit, and a viewer that shows the full 0-65,535 range makes them look dark. The data is fine: adjust brightness and contrast (Image › Adjust › Brightness/Contrast in Fiji) rather than converting to 8-bit, which throws information away.

Why won’t my CZI open in Fiji on a Mac?

Many CZI files are JPEG-XR compressed, and Bio-Formats cannot decode JPEG-XR on Apple silicon Macs, according to QuPath’s documentation. Convert on a Windows or Intel computer, or use SlideScope, which reads CZI with its own bundled JPEG XR decoder on both Windows and Mac.

How do I convert a whole folder of CZI files?

In ZEN, use Processing › Batch with the Image Export method. With bfconvert, loop over the files in a shell script. In SlideScope, open the folder, select the files and run “Export the selected files…” for one OME-TIFF per file, or “Extract scenes from the selected files…” for one file per scene.

Is SlideScope free?

SlideScope is a paid app with a free preview (open, measure and annotate a few of your own images) and a 3-day free trial.

Free preview: open, measure and annotate up to 5 of your own images. No account or card needed. Export, sharing, comparing slides and AI Analysis come with the 3-day free trial: $0 today, then $25/month unless you cancel before it ends. PayPal or card required, and you can cancel anytime from your account. Annual billing is available at $249.99/year, which works out to about two months free.

Convert without uploading

Open your own CZI files with the free preview, then export lossless OME-TIFF with the 3-day free trial. Already decided? Subscribe now.

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