3

I need to read a .ndpi format image using OpenSlide. However, it doesn't seem to be working and I'm receiving an error. I'm running this on google colab.

import openslide
import matplotlib.pyplot as plt
import numpy  as np
import cv2
path = "/content/02_HER2.ndpi"

def get_level(slide, level):
    return slide.read_region((0, 0), level, slide.level_dimensions[level])

slide = openslide.OpenSlide(path)
#plt.imshow(np.array(get_level(slide,3)))

img_slide = np.array(get_level(slide,3))
plt.imshow(img_slide)
plt.show()

And this is my error:

 OpenSlideUnsupportedFormatError           Traceback (most recent call last)
<ipython-input-9-09712eaa5bea> in <module>()
      8     return slide.read_region((0, 0), level, slide.level_dimensions[level])
      9 
---> 10 slide = openslide.OpenSlide(path)
     11 #plt.imshow(np.array(get_level(slide,3)))
     12 

1 frames
/usr/local/lib/python3.6/dist-packages/openslide/lowlevel.py in _check_open(result, _func, _args)
    172     if result is None:
    173         raise OpenSlideUnsupportedFormatError(
--> 174                 "Unsupported or missing image file")
    175     slide = _OpenSlide(c_void_p(result))
    176     err = get_error(slide)

OpenSlideUnsupportedFormatError: Unsupported or missing image file
Sahithi
  • 31
  • 2

1 Answers1

1

Tracing the error, the file seems to be unsupported or missing. Now, Openslide supports "ndpi" files, so I would check to make sure your file is not corrupted or damaged in any way.

Also, make sure that there were no issues while uploading the file to Google Drive. Sometimes, you can end up with broken or incomplete files if not careful in this process.

Have you tried loading up this image in other ndpi viewers such as Aperio Technologies ImageScope (Windows), NetScope Viewer (Windows), NDPITools (cross-platform) etc. ? This will tell you if the file is good to go.

Hope this helps.

Ani
  • 36
  • 4