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CZI Converter
Convert CZI microscopy images without the acquisition software, or a licence for it. Everything runs locally on an ordinary Windows PC.
How to Convert .czi Files in Bulk
1. Install reaConverter
2. Select CZI Files
3. Start Conversion
Step by step
See It in Action
For quick and effortless CZI file handling on your PC, reaConverter offers powerful conversion tools with batch processing. Best of all, it works entirely offline — ensuring your sensitive data never leaves your computer.
Extra Tools
Do more with your files
Converting CZI files for use in a larger project? reaConverter offers many ways to process files, so you can customize them according to your requirements.
Our range of editing options includes auto-processing options such as auto-rotate, auto-crop, watermarking and more. Change Color Space, copy Metadata, set DPI, manage ICC Profile, control Bit Depth.
User reviews
From those who tried it
Average User Rating:Last updated on June 29, 2026
Questions & Answers
CZI files: Frequently Asked Questions
What are CZI files?
CZI stands for Carl Zeiss Image, the proprietary file format written by ZEISS ZEN software on confocal, widefield and light-sheet microscopes, as well as Axio Scan slide scanners. A CZI file is multidimensional: a single file can hold several fluorescence channels, a stack of focal planes, a time-lapse sequence and a mosaic of stitched tiles, all alongside detailed metadata describing objectives, filters, pixel size and acquisition settings. Because the format is specific to ZEISS, CZI files usually cannot be opened outside ZEN or software built on the Bio-Formats library, which makes conversion to TIFF or PNG the common route for sharing images, preparing figures for publication and long-term archiving.
Can reaConverter open CZI files?
reaConverter fully supports the CZI file format – open, edit, and export CZI files to any other popular file format with ease.
How do I change CZI to another format?
reaConverter is a user-friendly tool for converting CZI files. Once installed on your computer, it allows you to convert all your .czi files at once with just a few clicks. You can even convert czi images directly from Windows Explorer using the right-click menu — fast and convenient.
Can I convert CZI online?
If you only want to convert a few CZI files, you are welcome to try our free online CZI converter.
How can I turn CZI files on my computer to another format?
The best way to convert CZI files on your PC is to get a quality piece of software, such as reaConverter. This software is extremely efficient in managing a wide range of batch files conversions, including conversion from CZI.
How can I automate CZI files conversion?
reaConverter supports all the essential automation features, such as right-click сonversion and Watch Folders, for the most efficient automated file conversion in any software of its kind.
Can I convert CZI files using scripts or the command-line interface?
reaConverter provides full access to all its features from the Windows command-line shell, including the command-line czi converter.
What else can I do with reaConverter?
Convert DICOM imagesCrop photoConvert GIS filesConvert Gerber imagesChange image color space
What formats can I convert a CZI file to?
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Beyond CZI conversion
Convert .czi files in batches of any size, with editing and processing applied along the way. The same tool also handles 700+ other formats, including CAD, medical imaging, and GIS.
