Free online CZI to OME.TIFF converter

What the CZI format is

CZI is the Zeiss Carl Zeiss Image container used by ZEISS ZEN and related microscopy systems. It can store multi-channel, z-stack, time-lapse, tiled, stitched, and high-bit-depth acquisitions together with calibration, objective, channel, and acquisition metadata. You typically encounter it after collecting data on ZEISS microscopes or receiving datasets from a laboratory that uses ZEN.

What the OME-TIFF format is

OME-TIFF is a TIFF image accompanied by OME-XML metadata describing dimensions such as X, Y, Z, channels, time points, and image series. It is intended for interoperability with Fiji, Bio-Formats, OMERO, napari, QuPath, and other scientific imaging software.

OME-TIFF is useful when an application cannot open CZI, when metadata must follow an open specification, or when an analysis pipeline expects TIFF input. It can preserve multi-page and multidimensional data more reliably than exporting individual display screenshots, although the exact metadata retained depends on the reader and writer.

How to convert CZI to OME-TIFF

Using Fiji and Bio-Formats

1. Install Fiji, which includes the Bio-Formats importer and exporter.
2. Open the source with File → Open and select the .czi file.
3. In the Bio-Formats Import Options dialog, keep the original multidimensional structure where required. Enable View stack with ImageJ or open as a hyperstack; avoid converting to a single 8-bit plane if the original bit depth matters.
4. Use Plugins → Bio-Formats → Bio-Formats Exporter.
5. Select OME-TIFF as the output format, choose the required series, set lossless compression such as LZW if available, and save with a name such as sample.ome.tiff.
6. Reopen the result in Fiji and check the channel count, Z slices, time points, pixel type, and physical pixel sizes before using it for analysis.

Using the Bio-Formats command line

The Bio-Formats command-line utility bfconvert is suitable for repeatable conversions and batch processing. A basic conversion is:

bfconvert input.czi output.ome.tiff

To convert only the first image series and use lossless LZW compression, use:

bfconvert -series 0 -compression LZW input.czi output.ome.tiff

Quote paths containing spaces. For files containing several series, inspect each series and convert the required ones rather than assuming that the first series contains the complete experiment. The exact command-line options depend on the installed Bio-Formats version; run bfconvert -help to view them.

Using 101convert.com

You can also convert the file on 101convert.com for free without installing software. This option is convenient for a single file, but verify the output dimensions, metadata, and file size after downloading, especially for large microscopy datasets or files containing sensitive research data.

Quality, compatibility, and limitations

Choose lossless compression such as LZW or uncompressed output when pixel values must remain unchanged. JPEG compression can alter quantitative measurements and should not be used for analytical microscopy data.

A CZI may contain proprietary acquisition details, stage positions, instrument settings, annotations, thumbnails, attachments, or several related series. OME-TIFF normally preserves the image planes and standard OME metadata, but it may not preserve every Zeiss-specific field. Keep the original CZI as the archival master.

Large datasets can exceed classic TIFF limits or create very large output files. Use a BigTIFF-capable Bio-Formats version when the output exceeds 4 GB, and confirm that the receiving application supports BigTIFF and the selected OME-TIFF layout. Do not flatten channels, Z slices, or time points unless the target program requires a two-dimensional image.