SlideScope opens Zeiss CZI files natively on macOS 14 or later, on Apple Silicon and Intel Macs: every scene, channel, Z plane and time point, with the pixel size the file records. It exports the scene you are viewing, or every scene, to one OME-TIFF file. ZEN lite, the free ZEISS viewer, runs on Windows only.
Scenes, channels, Z and timeOME-TIFF exportApple Silicon and Intel
Get SlideScope on your Mac
Download the macOS build that matches your Mac: Apple Silicon (M-series) or Intel. The download page recommends the right one.
Open the DMG and drag SlideScope into Applications. The macOS install guide shows every step with screenshots, including what to do if macOS asks you to confirm the first open.
Sign in with a free account. Free preview: create a free account, sign in, and open up to 3 of your own local images. No card needed. The full 3-day trial, which includes export, starts only when you choose it.
Multi-scene CZI files: view every scene and export OME-TIFF
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.
Watch the whole workflow (1 min 41 s)
Opening a two-scene CZI, switching scenes, XY Overview, channels, Details, exporting one scene and every scene, and reopening the OME-TIFF. Narration in English; captions in every site language. Rendered from SlideScope 1.8.56 on Windows; the macOS build has the same controls.Transcript
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.
Step 1
Open the CZI file
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.
Step 2
Step through the scenes
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.
Step 3
See every scene in XY Overview
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.
Step 4
Check channels, pixel size and metadata
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.
Step 5
Choose File › Export Current Image as TIFF
Choose File › Export Current Image as TIFF… (Ctrl+Shift+C). Pick a folder and a name; SlideScope suggests one that ends in .ome.tif.
Step 6
Export one scene, or every scene
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.
Step 7
Open the result
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.
What the exported OME-TIFF contains
One file. Exporting the scene on screen writes one image; exporting from XY Overview writes every scene as a separate image inside the same file, each at its own size. It does not create one file per scene.
The pixels are written unchanged, with lossless compression (Deflate). Brightness, contrast and gamma are display settings and are not applied to the export.
Pixel size in micrometres, the Z step when there is a Z stack, the channel names recorded in the CZI and the channel colours currently set in the viewer. A file without a recorded pixel size exports without one; SlideScope does not invent a calibration.
Resolution: scenes that fit in memory are exported at full resolution. A large tiled scan, such as a slide scanner region, is exported at its overview resolution. The confirmation names the ratio, for example 1:8, and the recorded pixel size is scaled to match. The full-resolution scan stays viewable region by region in SlideScope.
A single exported image wider or taller than 4,096 pixels also gets reduced-resolution pyramid levels. A file with several images does not. Files above 2 GiB are written as BigTIFF.
Not copied: the rest of the CZI acquisition metadata, and scene positions as stage coordinates. Keep the original CZI as the archival file.
What you need
Windows 10 or 11, or macOS 14 or later on Apple Silicon or Intel. Free preview: create a free account, sign in, and open up to 3 of your own local images. No card needed. Export needs the 3-day trial or a subscription ($25.00 per month after the trial).
If something looks wrong
Only one scene appears
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.
The colours differ from ZEN
Channel colours come from the file where it records them. Change them in Display › Channel colour…; the export records the colours you set.
The export is smaller than the scan
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.
Export asks you to start a trial
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.
How well CZI support is tested
In our published format test, run on 2026-09-18, all 48 of 48 CZI files opened, with up to 8 channels, 56 Z planes and 10 time points; the largest was 4.5 GB. It is our own test of the shipping loaders, published with its raw data, not an independent certification, and the sample files are not every CZI variant in use. Public test files include multi-scene well plates and tile regions but no multi-scene slide-scanner CZI, so that case has less coverage. See the format benchmark and the compatibility reference.
Other ways to open CZI on a Mac
Tool
Good for
Keep in mind
SlideScope
Opening, reviewing, measuring and exporting CZI files on a Mac, alongside ND2, SVS and other formats.
A viewer and review tool. No scripting or custom analysis pipelines.
Fiji / ImageJ with Bio-Formats
Free, open-source analysis with plugins and macros; reads CZI on macOS.
An analysis platform; each scene is imported as a series through an import dialog.
QuPath
Free whole-slide analysis; reads CZI through Bio-Formats.
Built around slide analysis projects rather than quick review of multidimensional stacks.
ZEISS ZEN lite
The vendor’s free viewer, closest to the acquisition software.
Windows only, so not an option on a Mac without Windows.
Questions
Can I open CZI files on a Mac?
Yes. SlideScope opens CZI files natively on macOS 14 or later, on Apple Silicon and Intel Macs, including files with several scenes, channels, Z planes and time points. Fiji with Bio-Formats also opens CZI on a Mac. ZEN lite, the free ZEISS viewer, is a Windows application.
How do I see every scene of a CZI file?
Use the Scene control under the image to step from scene to scene, or turn on XY Overview to see every scene at its recorded position. Each scene keeps its own size and name.
Can I export a CZI scene to OME-TIFF?
Yes. File › Export Current Image as TIFF exports the scene on screen, or every scene when XY Overview is on. Every scene becomes its own image inside one OME-TIFF file, with lossless compression, pixel size and channel names. Export needs the free trial or a subscription.
Is SlideScope affiliated with ZEISS?
No. SlideScope is independent and is not affiliated with ZEISS. Product names describe file-format and comparison intent only.
SlideScope is not affiliated with ZEISS. ZEISS, ZEN and CZI are named to describe file compatibility. SlideScope is for research, education and review, not for diagnosis.
Try it on your own CZI file
Free preview: create a free account, sign in, and open up to 3 of your own local images. No card needed. Full access, including export: 3-day trial, then $25.00 per month.
