.czi to .tiff conversion


#1

Hey everyone! How do I convert a .czi file to single channel .tiff files in Fiji ImageJ?


#2

Hey @Kate_M,

Please have a look at this wonderful feature in ImageJ / Fiji (see “convert”):
https://imagej.nih.gov/ij/docs/guide/146-29.html#toc-Subsection-29.12

You have an option to read files using Bio-Formats.

Best,


#3

Hi all,

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.

Best

Oli


#4

HI
I could not open the CZI images


#5

Hi Shaista,

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:
https://docs.openmicroscopy.org/bio-formats/5.7.1/about/bug-reporting.html

Here is the compatibility table:
https://docs.openmicroscopy.org/bio-formats/5.7.1/supported-formats.html#term-ratings-legend-and-definitions

Best,