Thanks for the reply. I suspect our best bet is to ask our colleagues to provide smaller images. Bio-Formats under ImageJ seems to work just fine - except that the dimensions are too large for ImageJ.
You don't mention it - but I'll add it here for completeness: QuPath can open and display the files, but only shows ONE image from each stack in the file. -- Kenneth Sloan [email protected] Vision is the art of seeing what is invisible to others. > On Mar 21, 2026, at 15:43, Fred Damen <[email protected]> wrote: > > Greetings, > > I google(d) 'imagemagick .czi file' and came up with a few libraries/tools > for reading/converting .czi files. Most in/with Python, so you could roll > your own import plugin. > > R Package (readCzi): Use the readCzi package to read and convert CZI files > to TIFF, with options for projection and normalization. > > ZEN Software: Use Zeiss ZEN software (including Lite) to export CZI files > to more universal formats like TIFF. > https://www.zeiss.com/microscopy/en/products/software/zeiss-zen/czi-image-file-format.html > > Python: Use libraries such as aicspylibczi or aicsimageio to read CZI data > and metadata, which can then be processed or saved using ImageIO or > OpenCV. > > Alternative Tooling: Use czi-tools (which may use vips or ImageMagick > internally) to read specific regions or convert CZI files. > > Enjoy, > > Fred > > On Sat, March 21, 2026 12:44 pm, Kenneth Sloan wrote: >> QuPath *almost* works. >> >> The .czi file includes several STACKS. QuPath only opens ONE image from a >> given stack. >> >> Any clues? >> >> (Running on Mac, using Intel version - as I read the blurbs, .czi is not >> supported on the Apple Silicon version). >> >> -- >> Kenneth Sloan >> [email protected] >> Vision is the art of seeing what is invisible to others. >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
