I am working on an application wherein I need to support Fiji+bioformats for opening medical file formats. I tried 2 methods.
Using ImageProcessorReader from the package (" import loci.plugins.util.ImageProcessorReader") of bioformats.jar in my java code. The plan was to be able to pick this package up from the fiji bioformats folder, but I cannot find the jar file inside. The loci_plugins jar is missing.
Then I was trying to use ImageReader to get the slice of the plane and Java code threw an exception of “java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory”. This jar is also missing in Fiji bioformats.
My question is how is Fiji using Bioformats to read the files. I cannot get it to work with:
File Reading using bioformats loci plugin.
File Reading using bioformats from fiji only.
Both of these have unresolved dependencies.
Thanks for the help.