Hey everyone! How do I convert a .czi file to single channel .tiff files in Fiji ImageJ?
Please have a look at this wonderful feature in ImageJ / Fiji (see “convert”):
You have an option to read files using Bio-Formats.
We had made a small script to extract LIF files in a given folder. I’ve modified it and it should work with CZI files, feel free to give it a shot. If you experience any problems, please post an example CZI file so that I may debug the issue.
I could not open the CZI images
I know my answer comes late, but is it coming from a recent version of your Zeiss software?
Did you check that everything is up-to-date with ImageJ + plugin?
You have the ability to report an error to Bio-Formats guys when you encounter some trouble opening your images:
Here is the compatibility table: