FiJi macro for batch processing OMX files in SIM check
This is a Fiji macro written around 2015 for the group of Simon Foster@UoS to help batch process files acquired on an OMX microscope. It requires SIM reconstructed files (raw OMX data will not work) and the SIM check plugin has to be installed in your Fiji installation.
Instructions:
- Have all your files in one folder.
- Make sure to have an output folder.
- The macro will threshold all the files in the folder to enable fast transformation of files to be shown in presentations/figures.
Note: Ensure that you have the SIM check plugin installed in your Fiji setup for the macro to work properly.