Batch converstion of nd2 files

[ramaniak]

Hello,
Is there any way to batch convert nd2 sequence files to tiff/jpeg formats. The Nis Elements Viewer does this well if you have just a few sequence files. I have a few hundred files that need to be converted and it is proving to be a tedious process. I am also trying to find a batch process so that the conversion process is easy in the future as well.
I tried using bfconvert with the latest version of loci_tools, but this seems to have issues with the current nd2 formats. There does not seem to be any other batch conversion apps that I can find. Any help would be much appreciated.

I am on a Mac but have access to windows machines.

Thanks

[mlinkert]

bfconvert is the recommended way to do conversion on the command line.

We can almost certainly fix the problems with the .nd2 files, but we need to know exactly what the issue is. Do you see an error message? Do the converted files contain incorrect images or metadata? Are you using the latest version of Bio-Formats (4.4.6)?