Other alternatives for CZI to TIFF conversion

 The issue: I have received some comments after my last post where readers have suggested alternative freeware for converting czi to tif files that are not Matlab based. In this post, I will mention some of these. 

Alternatives: So, besides the functions I suggested on my last post, here are some alternatives.

1. Horst Obenhaus has suggested a Fiji plugin from Cristopher Leterrier that converts czi files to tif stacks and do some post-processing tasks. You can check the Github link here. The tutorial of how to use this code can be read here. Horst wrote that he has used it, so I see it as a trusted source.

2. Haagen Waade sent me a link to a Github page containing a Python coded czi2tif converter, written in November 2019 by Scott Warchal. I have not and do not know anyone who has tested this code yet, but I am curious to try it. Just by reading the code, I have the impression that it can also batch process czi files in the same directory, so it would make it equivalent to my Matlab code. I can write an update as soon as I find time to test it.

 3. For the readers working at my work place, that is, the Kavli Institute for Systems Neurocience (NTNU, Trondheim, Norway), there is an internal software repository in one of the network drives that all employees have access to. If you map the NTNU network drive as T:, then the directory is the following:

 T:\mh\kin\software\lab\Zeiss\CZI2TIFF_BatchConverter

In it there are two executables:

    CZItoTIFFConverterConsole.exe

    CZItoTIFFBatchConverter.exe

The first can be used through the command prompt, while running the second will open a GUI that permits the user batch process czi to tif conversions. Using the two is easy and there is a PDF file in the same folder which can guide you through the process (CZItoTIFFConverter.pdf). However, this software is old (2014) and is primarily (if not only) designed for czi files produced by Zeiss Axio.Scan.Z1 model. I tested it for that purpose and it worked fine (although it is a bit slow and it crashes occasionally). I tried to convert a confocal LSM 880 czi file recently with it, without success. Its origin is shrouded in mystery, being referenced to me by a past colleague who used it frequently. I saw it mentioned on an old reference in a Zeiss microscopy forum. You can download it through the link here. 

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