.czi to .tiff conversion

imagej

#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,


#6

@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


#7

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

Best

Oli


#8

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?


#9

@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?


#10

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?

Best,
Owen


#11

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?

Best