I’ll phrase this as a question but it is probably more of a feature request.
I often use the bioformats commandline tools to split/convert images from a range of microscopes into individual
.tif-slices before running my own python scripts or Cellprofiler pipelines on those slices.
As an example, this would split a large lif files from a multi-position, time-lapse experiment into many individual tif files.
bfconvert some_large_.lif "/scratch/im_W%s_T%t_C%c.tif"
This works fine, but working with folders that contain many thousands of images
becomes unwieldy, especially on network shares.
If I use the following command, the output will be correctly placed into subfolders
well_W%s, provided these folders already exist when I call the command.
bfconvert some_large_.lif "/scratch/well_W%s/im_W%s_T%t_C%c.tif"
Is there a
bfconvert option that will create any subfolders in the output path if necessary?