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