Using CZI files within the Medical Image Labeler

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?

Answer 1

[Madheswaran]

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!

Answer 2

[Prasanna]

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:

• https://bio-formats.readthedocs.io/en/v7.3.0/users/matlab/index.html
• https://fiji.sc/
• https://github.com/allencellmodeling/aicsimageio