Julia application to convert mrxs files to a OME-TIFF pyramids. All credit goes to glencosoftware (https://github.com/glencoesoftware), who wrote the bioformats2raw and raw2ometiff applications that are at the heart of this application.

Julia is required. Java 8 or later is required.

libblosc (https://github.com/Blosc/c-blosc) version 1.9.0 or later must be installed separately. The native libraries are not packaged with any relevant jars. See also note in jzarr readme (https://github.com/bcdev/jzarr/blob/master/README.md)

• Mac OSX: brew install c-blosc
• Ubuntu 18.04+: apt-get install libblosc1

bioformats2raw (https://github.com/glencoesoftware/bioformats2raw) and raw2ometiff (https://github.com/glencoesoftware/raw2ometiff) need to be installed and working.

1. Clone the repository:

   git clone https://github.com/leonardromano/mrxs2tiff.git

2. (Optional) Download sample .mrxs files used for testing (while in project folder):

   git submodule update --init

Modify the script file main.jl, specifying all the needed options (described there in detail) and run it using:

julia main.jl

To credit the mrxs2tiff software, please star the repository on GitHub. If you use the mrxs2tiff software as part of your research, teaching, or other activities, I would be grateful if you could cite my work. To give proper academic credit, follow the link for BibTeX export:

The converter is distributed under the terms of the GPL license. Please see LICENSE.txt for further details.