I am trying to open an .SLD file in python bioformats but to no avail. The .SLD I am testing my programme on has two series, and in each series there are 50 time point images, each of which is a 100-frame Zstack.
This is the code I use:
file_path = '/file/path/to/file.SLD' javabrdige.start_vm(class_path=bioformats.JARS, run_headless=True) im = bioformats.ImageReader(file_path) javabridge.kill_vm()
and this is the output i get:
Exception in thread "Thread-1" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:659) at java.util.ArrayList.get(ArrayList.java:435) at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654) at loci.formats.FormatReader.setId(FormatReader.java:1392)
please note that I have tried to run this with
headless=False and I get a similar output.
Also it might be worth mentioning that I can load single TIFs in just fine!
I have also tried to move my project to Matlab, using Bioformats in Matlab. I get the same error using bfopen(‘file_path_to_.SLD’).
Am i right in thinking the additional Slidebook update site in Fiji installs somethign important to get Bio-Formats working and this is missing in Python/Matlab hence these errors?
Any help would be greatly appreciated.