Would anyone know whether there exists a HDF5 reader for FIJI that operates in headless mode? Has anyone implemented batch analysis routines on data stored in HDF files in FIJI and can comment on how this was done?
What I would like to do
I am working with a custom database of images that are stored as separate datasets inside a single HDF5 file. The images are simply 2D arrays of ints (nothing fancy). I would like to batch process select images from the file using FIJI’s headless mode. The reason for wanting to work from the command line is that my full analysis pipeline utilizes different programs and languages which I glue together with bash scripts.
Possible solutions to my problem
I have tried the plugin from Uni. Freiburg lmb.informatik.uni-freiburg.de/resources/opensource/imagej_plugins/hdf5.html but it seems only to work with the GUI.
A rather inelegant solution would be to read the images from the HDF file and write them as separate TIFFs using a separate program, then open the TIFF’s in FIJI for processing.
Thanks everyone for your input!