.czi to .tiff conversion

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

Hey @Kate_M,

Please have a look at this wonderful feature in ImageJ / Fiji (see “convert”):

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


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.



I could not open the CZI images

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:

Here is the compatibility table:


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@oburri The code works like a charm! But it gives me 8 bit tiff files, I am wondering how to tweak it to obtain a monochrome single channel 16 bit tiff for each tile

That is a bit surprising, what is the original format of your data?



Sorry I thought I was dealing with 16-bit original data, It’s not surprising then…any recomendation about how to export 8-bit RGB tiffs then?

@oburri Also, this is not related but some of the images I take are not strictly a rectangular tiling (to save microscopy time I image around the borders of the tissue and some corners are missing). is there way to either add completely black images to fill in the gaps or fix the image labelling so that stitching process has the correct left to right order?

Hi Oli, the script works brilliantly but is saving each image as an individual file. Could you suggest an amendment that would save all converted czi files to one destination?


Hi @Owen_Connolly,

I’m afraid I don’t understand. You have several czi files? How do you want to save them?

EDIT: I think I understand,
Perhaps check line 20,
is_save_individual_planes = true;

If you set that to false, it might do what you want?


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Hi Oli, is there a way to export all channels by themselves in their colors (for me all single files show the same color) and also a merge? Thanks


The color of the images is on line 55
This means that bioformats tries its best to find the colors as they are in the file. If they show up as the same colors, then it was not able to do it and this script doesn’t try to customize the colors…

We do have an ActionBar called “Channel Tools” that does this for you after the export is done.

There are instructions here on using and installing it.