Can't open .czi stacks

Hello,

I am a new user of Icy, so I probably missed something. I want to work on fluorescence stacks taken with Zeiss software, so the extension file is a czi. Unfortunately, I can’t open the stack except with the imageJ panel. Is there any possibility to use such a file format directly with Icy?

Thank you very much !
Cyntia

Dear Cyntia,

Icy can open .czi images. Behind the hood, it uses the Bioformat library, which supports a great number of microscopy image formats.

I would need some more information to help you.

  • I would like to know which version of Icy you are using. You can find this information in the Output tab on the side panel on the right of the graphical user interface. You should see something like this:
    Output_tab
    In this screenshot, the version of Icy is 2.1.4.0.

  • I would also like to know how you tried to open the image

If you tried only one of this two options, could you try the other?

  • Last but not least, what is the size of your .czi file? And how much memory is Icy allowed to use?
    You can find information about memory in the Preferences menu (upper right corner, :hammer_and_wrench: icon). In the example below, I see that the computer has 16 Go of memory (max value in parentheses) and that Icy is allowed to use 14 Go (value in the dialog box on the right).

Best regards,
Marion

2 Likes

Hello Marion,

I currently use the version 2.1.3.0 of Icy under Ubuntu 18.04. If I drag and drop the file, or open it with the main menu, I got the same error message displayed here in red.

My stack is about 10.8 GB, whereas my max memory is 13 GB. I increased the available memory for Icy to 12 GB, and it’s still not working.

As all my error messages look linked to Java, I guess something might be wrong with my libraries, especially the VTK one. I have currently installed it, but can’t find the root folder.

1 Like

Dear Cyntia,

Thank you for sharing the error message!
I think there is two issues here: one with the VTK library and one with the opening of the .czi file. I don’t think they are related, but let’s invite @Stephane to join the discussion and get his opinion on this.

Best regards,
Marion

1 Like

Hi Cyntia,

Indeed it seems to be related to the version of java you are using.
Can you try to remove your openJDK 11 and use Oracle JRE 8 instead if possible to see if that helps ?
We provide Oracle JRE 8 for linux in both RPM and TAR.GZ formats from our download page:
Icy Download page

And you can find installation instructions here : JRE Installation for Linux Platforms

You can also follow instructions from thi spage if you want to use apt-get tool to install it :
Install java with apt on Ubuntu

Let us know if that fixed your problem :slight_smile:

Best,

– Stephane

1 Like

Hi Stephane,

As after adjustments I still couldn’t open the files, I switched on Windows 10, where Icy clearly indicates that the VTK libraries are loaded and the java environment is the 8 one. Icy version is the 2.1.4.0, and the ram is still about 120Gb. Both drag and drop or opening with the main menu lead to the same error message that I attached here.

Maybe I should give you one of the file to give a try?

Thank you very much for your help
Regards,

Cyntia

error_czi.png

icy_version.png

2 Likes

Hi Cyntia,

Looking at the error detail, it may be an issue with the version of Bio-Format (the Image reader library) that we are using in Icy (version 6.3.1). What surprise me though is that it works when you try to open it through ImageJ… maybe you’re using a different version of Bio-Format in ImageJ.
Indeed it would be really helpful if you can share a dataset with us that can reproduce the problem :slight_smile: Thanks.

Best,

– Stephane

1 Like