What this video covers
A ZEISS .czi file can hold several scenes: the wells of a plate, tile regions or the scan regions of a slide. This walkthrough opens a two-scene CZI in SlideScope, steps through each scene, and shows where each was recorded with XY Overview.
It then checks the channels and pixel size, exports one scene or every scene to OME-TIFF, and reopens the result. The exported files keep the pixel size and channel names, so Fiji, QuPath and other Bio-Formats readers open them correctly.
Prefer to read? How to open CZI files, including multi-scene files.
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.
The free trial includes every feature, export too, with just a free account.
When the trial ends, a subscription keeps everything working.
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.