"OpenSlideError: Cannot read slide position info: Expected 1 value" opening MIRAX data #159
Description
Context
Issue type: compatibility
Operating system : Windows 11, Google Colab
Platform (e.g. 64-bit x86, 32-bit ARM): 64-bit x86, Google Colab
OpenSlide Python version: openslide-python-1.1.2
Slide format (e.g. SVS, NDPI, MRXS): MRXS
Details
Dear Openslide Python,
first of all I want to say thank you for developing and maintaining this unique interface for reading virtual slides!
However, I have a problem when it comes to open MRXS files with Openslide. I know that MRXS is a very problematic format and there are lots of discussions around it but unfortunately I have lots of scanned slides in this format and I am desperately trying to make use of them...
I use OpenSlide on Google Colab and used the following code:
from openslide import open_slide
import openslide
from PIL import Image
import numpy as np
from matplotlib import pyplot as plt
path= './drive/MyDrive/DigitalSlide_E10M_2S_1_10-6-2021_04-31-03.mrxs'
slide = open_slide(path)
In the end I get the following error:
---------------------------------------------------------------------------
OpenSlideError Traceback (most recent call last)
<ipython-input-24-41a0213c9dad> in <module>()
1 path= './drive/MyDrive/DigitalSlide_E10M_2S_1_10-6-2021_04-31-03.mrxs'
----> 2 slide = open_slide(path)
2 frames
/usr/local/lib/python3.7/dist-packages/openslide/__init__.py in open_slide(filename)
386 object for other types of images."""
387 try:
--> 388 return OpenSlide(filename)
389 except OpenSlideUnsupportedFormatError:
390 return ImageSlide(filename)
/usr/local/lib/python3.7/dist-packages/openslide/__init__.py in __init__(self, filename)
158 AbstractSlide.__init__(self)
159 self._filename = filename
--> 160 self._osr = lowlevel.open(filename)
161
162 def __repr__(self):
/usr/local/lib/python3.7/dist-packages/openslide/lowlevel.py in _check_open(result, _func, _args)
131 err = get_error(slide)
132 if err is not None:
--> 133 raise OpenSlideError(err)
134 return slide
135
OpenSlideError: Cannot read slide position info: Expected 1 value
I have already seen some ideas to make it work like converting MRXS to MRXS with the SlideMaster software but I does not work anymore. Is there any solution to tackle this problem?