extract metadata from VSI files

[LibbyLi667]

Hi there,

Just wondering if bioformats can deal with images in vsi format generated from VSlide (as I know the instrument generates image in vsi format along with other files in vsa, vsc, vsr, and vsv formats). I used 'get_omexml_metadata' for the vsi file but got error as below:

... 9 more
Traceback (most recent call last):
  File "/Users/xli677/Desktop/mytardis_ime/mytardis_ime/.venv/lib/python3.10/site-packages/javabridge/jutil.py", line 382, in run_script
    result = call(context, "evaluateString",
  File "/Users/xli677/Desktop/mytardis_ime/mytardis_ime/.venv/lib/python3.10/site-packages/javabridge/jutil.py", line 892, in call
    result = fn(*nice_args)
  File "/Users/xli677/Desktop/mytardis_ime/mytardis_ime/.venv/lib/python3.10/site-packages/javabridge/jutil.py", line 859, in fn
    raise JavaException(x)
javabridge.jutil.JavaException: Wrapped java.lang.IllegalArgumentException: Invalid series: 0 (<java-python-bridge>#11)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/xli677/Desktop/mytardis_ime/mytardis_ime/ime/metadata_extraction.py", line 50, in <module>
    xml_string_vsi = bioformats.get_omexml_metadata(inf_vsi)
  File "/Users/xli677/Desktop/mytardis_ime/mytardis_ime/.venv/lib/python3.10/site-packages/bioformats/formatreader.py", line 1041, in get_omexml_metadata
    xml = jutil.run_script(script, dict(path=rdr.path, reader = rdr.rdr))
  File "/Users/xli677/Desktop/mytardis_ime/mytardis_ime/.venv/lib/python3.10/site-packages/javabridge/jutil.py", line 399, in run_script
    raise JavaException(call(e.throwable, "unwrap", "()Ljava/lang/Object;"))
javabridge.jutil.JavaException: Invalid series: 0

Anyone got ideas? thanks.

Cheers,
Libby