Batch Processing LIF Files


I’m having a seemingly simple issue, yet I haven’t found a reasonable way of solving it.
I have been taking my Images with a Leica SP8 microscope, therefore all my Images were saved in a LIF Format. As far as I know Lif files are usually very compatible with FIJI, and I haven’t had any issues opening and working with them so far.
However now after writing my macros I tried to go into Batch Processing of these Images, yet when I try to do it via FIJI -> Process -> Batch -> Macro and then add my folder of Images to the Input section, only the first Image of the whole folder is being analyzed.

Any help on how to Batch process the Lif files (or easily convert them into tif files) would be appreciated, thank you!

Hi @marieschulte,

The issue might come from the fact that Bio-formats importer takes only the first serie within the lif. You can have a look to this script from @oburri.