My first Github upload: CZI to TIFF converter (Matlab)

The issue: Zeiss czi file format is not always the easiest when thinking of exporting and converting it to other formats. Zeiss provides a free version of their reader called ZEN lite, which permits all users to see and manipulate the acquired images. However, I have often heard users asking me how to convert or export their images into other formats (like TIF). That would make it easier to open and process them in standard commercially available software like Adobe Photoshop, for example. Although possible, this sort of conversion is not simple or straightforward to do when using the different versions of ZEN (black, blue, lite), and they are often different depending on the version. An even harder task is to batch this process, so users would have to repeat the same protocol manually for each file. 

Solution: I recently wrote my own pack of functions, collectively called 'czi2tiff' in Matlab, which I now make publicly available at my Github account. The link is: 

https://github.com/paulojor/czi2tiff.git

The main function from this pack is the file called 'czi2tiff.m' that converts czi files to tiff files. It was written with files produced by ZEN black software associated with the Zeiss LSM 880 in mind. I have also successfully tested it with some mosaic files produced by ZEN blue associated with a Axio-Imager.Z2. You can run this function by opening your Matlab environment (I used R2023a), selecting the folder containing the pack as your current directory and typing the name of the function. Upon running, a menu will appear that permits you to choose the czi file to convert. NOTE: you need to download Bio-formats matlab pack v7.0.0. and install it in the same folder as this functions, because some of the functions will use the bio-formats pack. 

The function will convert the original czi file into the equivalent tiff files, one for each channel. the result file will have the same root name as the original, and it will be stored in the same folder. 

'czi2tiffBatch.m' is the equivalent batch converter. When running this function, a menu will show up and ask which folder to process. All czi files inside the chosen folder will be converted to their tiff equivalents. 

So far, I tested it with files up to 1.38 GB size and some of them contained both z-stacks and tiled (mosaic) images. 

This is my first Github upload, so it may have some issues. Feel free to download and test it. Write me if you find any errors or have comments about the code and the way it is used.   


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