You can open ZEISS CZI files with ZEN lite, ZEISS’s free viewer for Windows; with Fiji or QuPath, which are free and read CZI through Bio-Formats on Windows, Mac and Linux; or with SlideScope, a desktop viewer for Windows and Mac with a free trial. On Apple silicon Macs, Bio-Formats cannot read JPEG-XR-compressed CZI files. The steps below use SlideScope.
A CZI can hold several scenes: the wells of a plate, tile regions, or the scan regions of a slide. SlideScope shows each scene on its own or all of them together, and exports the scene you are viewing or every scene to OME-TIFF. The video and the steps below use a public two-scene sample file.
A CZI file can hold several scenes: wells of a plate, tile regions, or scan regions. Here is how to view each one, and export them as OME-TIFF.
A CZI with two scenes, opened directly. No conversion. The Scene control steps from one scene to the next. Scene 2 is well D7. Scene 1 is well D6. The XY Overview places every scene where it was recorded. These two wells sit 9 mm apart.
Blend the channels into one view. Switch a channel off to see what it contributes. Zoom in. The scale bar stays calibrated. Details lists the pixel size, channels and acquisition settings.
To export, choose File, then Export Current Image as TIFF. While you view one scene, only that scene is exported. Before it starts, you see the pixel size, channels and compression it will write. To export every scene, turn on XY Overview first. All scenes go into one OME-TIFF file. Each scene is its own image inside it.
Open the result. Both scenes are there, as image 1 and image 2. Pixel size and channel names came through.
A free account lets you open and view local images before any trial. Export needs the 3-day trial or a subscription. A large tiled scan exports at its overview resolution, not the full scan. It is the same app on macOS and Windows. This footage was rendered on Windows.
Choose File › Open File… (Ctrl+O on Windows, ⌘O on a Mac) or drag the .czi file onto the window. The first scene appears straight away. Nothing is converted and the file is not uploaded.
A file with several scenes shows a Scene control under the image. Use − and + or type a number. Each scene keeps its own size and its name from the file, such as a well (D6, D7) or a tile region.
Click XY Overview next to the Scene control, or choose View › XY Overview (Ctrl+Shift+X). Every scene is drawn where it was recorded, gaps included. Click a scene to select it and double-click to open it. Scenes that sit far apart, such as wells 9 mm apart, start as small tiles: zoom in to see them.
In Display, tick Blend channels into one view for a colour composite, or switch single channels off. Details lists the pixel size, dimensions, the current scene and its size. Brightness, contrast and colours change only what you see, never the stored pixels.
Choose File › Export Current Image as TIFF… (Ctrl+Shift+C). Pick a folder and a name; SlideScope suggests one that ends in .ome.tif.
While a single scene is on screen, only that scene is exported, with a name such as sample_scene-2.ome.tif. To export every scene, turn on XY Overview first: all scenes go into one OME-TIFF file, each as its own image at its own size. Before anything is written, a confirmation shows the size, the pixel size, the channels and the compression.
Click Open Exported TIFF when the export finishes. SlideScope shows each exported scene as an image; step through them with the Image control. OME-TIFF readers that support several images per file, such as Bio-Formats in Fiji, list them as separate series.
Windows 10 or 11, or macOS 14 or later on Apple Silicon or Intel. Free preview: open, measure and annotate up to 5 of your own local images. No account or card needed. Export needs the 3-day trial or a subscription ($25.00 per month after the trial).
Scenes become steppable when they share a pixel type and the same channels, Z planes and time points. If they do not, SlideScope shows the first scene and says why in Details. If that is not what you expect, send us the file.
Channel colours come from the file where it records them. Change them in Display › Channel colour…; the export records the colours you set.
A large tiled scan is exported at its overview resolution, and the confirmation says so before anything is written. The full-resolution scan stays viewable in SlideScope.
Viewing works with a free account. Export needs the free trial or a subscription.
Sample in the video and screenshots: S2_3x3_CH2.czi from the czitools sample data (Sebastian Rhode / ZEISS, GPL-3.0), two scenes of a 3 × 3 mosaic with DAPI and EGFP. No customer data.
| Tool | Cost | Platforms | Best for |
|---|---|---|---|
| ZEISS ZEN lite | Free (needs a ZEISS ID to download) | Windows | The vendor’s own viewer, closest to the acquisition software |
| Fiji / ImageJ with Bio-Formats | Free, open source | Windows, macOS, Linux | Analysis with plugins and macros; each scene imports as a series |
| QuPath | Free, open source | Windows, macOS, Linux | Whole-slide analysis projects and scripting |
| SlideScope | Free preview (no card), 3-day free trial, then a subscription from $25/month | Windows 10+, macOS 14+ (Apple silicon and Intel) | Viewing, measuring and annotating CZI alongside CZI, ND2, SVS, NDPI, MRXS, DICOM and TIFF, with files kept on your computer |
Open ZEISS CZI files in SlideScope on Windows or macOS without converting them first. Review the channels and image dimensions stored in your file. Local viewing does not upload the image.
Source: Whole slide image viewer comparison (platforms and prices, each linked to its source).
QuPath’s documentation says Bio-Formats does not currently support JPEG-XR compression on Apple silicon, and many CZI files are JPEG-XR compressed. Its suggested workarounds are converting the file on another computer or switching to the Intel build of QuPath. SlideScope does not use Bio-Formats for CZI: it reads CZI with its own bundled JPEG XR decoder in both the Windows and Mac builds.
Evaluate SlideScope when you need one desktop app that opens mixed microscopy files and quantifies standard objects on your own machine. Keep the original tool when you need microscope control, programmable image processing, scripted analysis pipelines, or institutional image management.
Fiji/ImageJ, QuPath, napari, CellProfiler: Extensible processing, macros, plugins, scripting, segmentation, batch measurement pipelines, pathology analysis, and scientific Python workflows.
OMERO: Centralized image repositories, permissions, collaboration, and institutional data management.
Yes. ZEN lite (Windows) and Fiji or QuPath with Bio-Formats are free. SlideScope is free to download with a free preview that opens, measures and annotates your own images (no card) and a 3-day free trial of every feature (PayPal or card required); after the trial it is a subscription.
Use macOS 14 or later. Choose the Apple Silicon or Intel download that matches your Mac, and copy the file to local storage before opening it.
Confirm the file finished copying. If it still fails, contact support with the app version, file format and error message so we can help investigate.
It is built for research labs, microscopy core facilities, educators, students, and pathology review teams that need practical file review, annotations, measurements, metadata, and export.
Read the original format documentation.
SlideScope is independent and is not affiliated with Leica Biosystems, ZEISS, Nikon, ImageJ, Fiji, QuPath, napari, CellProfiler, or OMERO. Product names are used only to describe factual comparison and alternative-search intent.
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