Reading compressed CZI on Linux/MacOS machines - Python czifile library.

Your place to discuss general handling of images and the CZI file format
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user-6898
Posts: 5
Joined: Thu Jan 01, 1970 1:00 am

Reading compressed CZI on Linux/MacOS machines - Python czifile library.

Post by user-6898 »

I find that a CZI file with compressed data (comp.mode=jpgxr) is read fine on a Windows machine using the czifile.py library.
However, on a Linux or MacOS machine, the ndarray data returned by the CziFile.asarray() function is zero-valued.

On the other hand, a CZI file with uncompressed data (comp.mode=uncompressed) is read fine on all OS platforms.

So is the following comment in a post elsewhere in this forum:
"Please be aware that you have to save the Axio Scan CZIs uncompressed in order to use the reader",
still valid?
user-4
Posts: 398
Joined: Thu Jan 01, 1970 1:00 am

Post by user-4 »

Dear nadukandi,

I’m very sorry, but the czifile.py library is not part of OAD and therefore we have neither in-depth experience concerning its features nor insights in its behavior on arbitrary operation-systems. Please contact the creator of the library.

Zeiss offers the ZeissImageLib (.Net-based) and the (non commercial) open source libCZI (c++ based, intended to work cross-platform). Both libraries are capable to open compressed images.

In addition to that we can recommend the Bio-Formats Reader. ZEISS and OME have put a lot of effort in this popular reader to open a wide span of czi images including compressed images.
user-6898
Posts: 5
Joined: Thu Jan 01, 1970 1:00 am

czifile depends on imagecodecs which I could build from source on RedHat Linux.

Post by user-6898 »

Thank you for your quick reply.
Reading the comments/documentation of czifile.py I found:
"czifile.py relies on the imagecodecs package for decoding LZW, JPEG, and JPEG XR compressed images."
Following this line, the notes of imagecodecs states:
"Imagecodecs is currently developed, built, and tested on Windows only. The API is not stable yet and might change between revisions. Works on little-endian platforms only."

I could build imagecodecs from source code and its various dependencies on a RedHat Linux virtual machine.
All is well.
--Prashanth Nadukandi.
Emma Brown
Posts: 2
Joined: Wed Apr 26, 2023 10:39 am

Re: Reading compressed CZI on Linux/MacOS machines - Python czifile library.

Post by Emma Brown »

I think that each different file will be saved at a suitable platform so you should research the platforms carefully before saving. slither io
Margo Barajas
Posts: 1
Joined: Fri Aug 25, 2023 6:35 am

Re: Reading compressed CZI on Linux/MacOS machines - Python czifile library.

Post by Margo Barajas »

My goal is to convert a 4-channel z-stack czi image into a single-channel z-stack tiff file. Since I have a large number of photographs to process, I hoped that using python would make the process go more quickly.

I tried to implement the above-mentioned code but ran into an error:

Error in calling OmeTiffWriter()geometry dash lite: NoArgumentsTypeError

So far, my attempts to read the manual have been unsuccessful.
Possible answers?
Perhaps there's been a development since 2020.
Michael Arrington
Posts: 1
Joined: Wed Aug 30, 2023 10:24 am

Re: Reading compressed CZI on Linux/MacOS machines - Python czifile library.

Post by Michael Arrington »

Your experience will likely be helpful for others facing similar issues with reading CZI files on io games non-Windows platforms.
A;ex Belfok
Posts: 1
Joined: Tue Sep 19, 2023 12:04 pm

Re: Reading compressed CZI on Linux/MacOS machines - Python czifile library.

Post by A;ex Belfok »

Ensure that your Linux or macOS system is up to date with the latest software updates and patches. Sometimes, compatibility issues can be resolved with OS updates. Maybe you need to view view hidden files in mac, I'll check more and get back.
Domte Banki
Posts: 1
Joined: Mon Oct 16, 2023 11:57 am

Re: Reading compressed CZI on Linux/MacOS machines - Python czifile library.

Post by Domte Banki »

Yes, the comment you mentioned regarding saving Axio Scan CZI files uncompressed in order to use the reader is still valid. It seems that the czifile.py library may have difficulty reading CZI files with compressed data geometry dash bloodbath (comp.mode=jpgxr) on Linux and macOS machines, resulting in zero-valued ndarray data.

In this case, to ensure compatibility and successful reading of CZI files on all operating systems, it is recommended to save the Axio Scan CZI files uncompressed (comp.mode=uncompressed). This will allow the czifile.py library to read the data correctly without any issues.
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