What this video covers
A ZEISS .czi file will not open on a Mac by double-clicking it, and ZEISS ZEN lite, the free vendor viewer, runs on Windows only. Fiji opens CZI through Bio-Formats on any platform, but it is an analysis platform. This video compares the options, then opens a real CZI in SlideScope.
You see the image pyramid load without converting the file, channels shown separately and as a colour composite, a Z-stack stepped plane by plane, the acquisition metadata, and a measurement in calibrated micrometres.
Prefer to read? How to open CZI files: every option compared.
Transcript
Updated since recording. Since this video was recorded, the free trial changed: it now covers 10 of your own images or 3 days, whichever comes first, and needs only a free account, no PayPal or card. Current prices are on the pricing page. See pricing.
This is a CZI file from a Zeiss microscope. Double-click it on a Mac and nothing happens.
ZEN lite is the free vendor tool, but it is Windows only.
Fiji reads CZI through Bio-Formats on Mac, but that is an analysis platform for one image.
Open the .czi directly. No import step, no conversion.
It reads the image pyramid, so it zooms without loading the whole file.
Pan around at full resolution. The scale bar stays calibrated.
Channels are listed on the left. Composite blends them in colour.
Toggle each channel independently to see what it contributes.
This file is a Z-stack. The slider steps through focal planes.
Metadata sits beside the image: objective, pixel size, acquisition settings.
Because it read the pixel size, measurements come back in micrometres.
To be straight about scope: this is a viewer. No segmentation, batch quantification or scripting.
It exports TIFF, so handing the region over is clean.
For research, teaching and review. Not for clinical diagnosis.
Same app on Windows 10 or later and macOS 14 or later, Apple Silicon or Intel.
Windows builds are code-signed through SSL.com.
A 3-day full-access trial, then $25.00 a month. Link is in the description.