Using CZI files within the Medical Image Labeler

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Jason
Jason 2024-6-14
回答： Prasanna 2024-7-25
I have some CZI files I want to use within the medical image labeler app, but this not currently an accepted file format. What would be the best way for me to convert them into a format the app can read?

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回答（2 个）

Madheswaran
Madheswaran 2024-7-12
Hi Jason,
Based on my current knowledge, MATLAB supports the DICOM and NIfTI file formats. However, I have discovered that there are user-created functions available that might enable the processing of CZI files.
The Open Microscopy Environment has created a MATLAB toolbox meant for processing various microscopy images.
http://www.openmicroscopy.org/bio-formats/downloads/
There are some submissions on the MATLAB File Exchange site as well that may be useful.
  1. This function specifically reads information from Zeiss CZI image file: https://www.mathworks.com/matlabcentral/fileexchange/58666-read-information-from-zeiss-czi-image-file
  2. This function reads multiple life science image formats including Zeiss CZI image: https://www.mathworks.com/matlabcentral/fileexchange/32920-imread-for-multiple-life-science-image-file-formats
Hope this helps!
Prasanna
Prasanna 2024-7-25
Some ways to convert CZI image to medical image labeller app compatible formats (DICOM) can be done using the following tools and plugins.
  • ImageJ/Fiji with Bio-Formats plugin: you can download and install Fiji from the official site and convert CZI images to DICOM images directly using the toolbar present.
  • Python with Bio-Formats and ‘Pydicom’ libraries: you can install required packages for python such as ‘aicsimageio’, and ‘pydicom’ and convert CZI to DICOM using the ‘FileDataset’ instance of the ‘pydicom’ library
  • MATLAB with the Bio-Formats library: you can download the bio-formats plugin package for MATLAB, read and convert CZI files to DICOM by reading the CZI file, creating a DICOM metadata structure and then writing the image data to a DICOM file.
For more information on the above tools/packages, refer to the following documentation:

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