View CZI files in your browser
The file Zeiss microscopes and slide scanners save, from confocal stacks to whole slides. Open one right here, each channel in its color. Nothing leaves your device.
Or drop it anywhere on this page
What you'll see
Your image opens with each channel in its own color, mixed as the microscope's software shows them, with Z, time and scenes on sliders.
- Channels • Each in its color with its own levels
- Z, time and scenes • A slider each
- Measure • Lengths in µm, with a scale bar
- Export • Save the view as PNG or the plane as OME-TIFF
About CZI
Zeiss's ZEN software saves every image its microscopes take as CZI: LSM confocals, Axio Observer and Imager stands, Lattice Lightsheet and Celldiscoverer systems, and Axio Scan slide scanners. Labs pass CZI files around as they came off the microscope.
A CZI is a file of segments. Each subblock holds a plane, a tile of a scan or a smaller copy of one, uncompressed or packed with JPEG XR or Zstandard, and an XML document beside them keeps the channels, their colors and wavelengths, the pixel's size in µm, the objective and when it was taken. A slide scan also keeps a picture of its label and of the whole glass.
Filepeek reads it in your browser, each tile from the file only when it shows. Channels are mixed in their colors on your graphics card, each with its own levels, Z, time and scenes go on sliders, a scan's tiles go where the file places them, Measure gives lengths in µm, and Export saves the view as PNG or the plane as OME-TIFF.
Carl Zeiss Image
.czi
Format
- MIME type
- application/octet-stream
- Made by
- Carl Zeiss Microscopy, for its ZEN software
Inside the file
- Pixels
- 8 or 16 bit, floats, or color
- Holds
- Channels, Z, time, scenes and tiles
- Packed
- JPEG XR, Zstandard or JPEG
- Metadata
- XML of the microscope and the run
Opens in every browser
Filepeek opens CZI in Chrome, Edge, Firefox and Safari. No browser shows it by itself.
- YouChromeOpens through Filepeek
- YouEdgeOpens through Filepeek
- YouFirefoxOpens through Filepeek
- YouSafariOpens through Filepeek
Apps that open CZI
- WindowsZEN lite, free • Fiji with Bio-Formats and QuPath, free
- MacFiji with Bio-Formats and QuPath, free
- iPhone and iPadNo app built in opens it
- AndroidNo app built in opens it
Questions
How do I open a CZI file?
Drop it on this page or press Peek a CZI. It opens with each channel in its color, with nothing to install, and even a scan of many GB opens, since only the tiles in sight are read.
Why is my CZI black in other apps?
Microscope cameras keep 12 or 16 bits, far more levels than a screen shows, and a dim stain sits in the lowest few. Filepeek sets each channel's levels from its own values, and Auto in Channels sets them again for the plane on show.
Can I look at one channel alone?
Yes. Channels lists each with its color, its wavelengths and its levels, and its box hides or shows it, so a DAPI stain and a GFP signal can be seen apart or together.
Does it open tile scans and slide scans?
Yes. A tile scan's tiles are put where the file places them, and an Axio Scan slide opens whole from the smaller copies it keeps, with its label and its picture of the glass under Images.
How do I go through the Z stack?
Drag the Z slider under the picture, or press the up and down keys. Time points and scenes get sliders of their own.
What if my CZI was saved in several parts?
ZEN can split a big acquisition into files named like name(1).czi. Each part opens on its own, with the planes it holds, and a note says so.