Stack Overflow
Stack Overflow

Questions tagged [openslide]

OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).

See also:

53 questions
8
votes
1 answer

Unsupported TIFF Compression

I'm using openslide-python to open a svs image, and I have run into the following issue: >> import openslide as osi >> a = osi.OpenSlide('image.svs') yields the error TIFFReadDirectory: Warning, Unknown field with tag 347 (0x15b)…
manan
  • 1,385
  • 13
  • 23
7
votes
2 answers

Is there any problem with the OpenSlide.read_region function?

I am using the python API of openslide packages to read some ndpi file.When I use the read_region function, sometimes it return a odd image. What problems could have happend? I have tried to read the full image, and it will be worked well.…
kinomoto-sakura
  • 71
  • 1
  • 2
5
votes
2 answers

How to generate heat map on the Whole Slide Images (.svs format) using some probability values?

I am trying to generate heat map, or probability map, for Whole Slide Images (WSIs) using probability values. I have coordinate points (which determine areas on the WSIs) and corresponding probability values. Basic Introduction on WSI: WSIs are…
Js541
  • 100
  • 1
  • 13
5
votes
2 answers

Openslide python import error

I am trying to use openslide's python bindings (http://openslide.org/download/) and have tried just about everything with no success in being able to import openslide to Python 2.7. Here's my error message: >>> import openslide Traceback…
Hunter Jackson
  • 53
  • 1
  • 3
4
votes
1 answer

How to merge tiles obtained using openslide-python

I am trying to combine tiles in the correct order so they end up as the same whole slide image (.svs file). The .svs file is read from a filepath according to the function beloew: def open_slide(filepath = None): try: slide =…
Tal Khan
  • 43
  • 3
4
votes
2 answers

How to display whole-slide Images (virtual slides) using the OpenSlide Python library? (Not using a web based viewer)

I am writing an application that can view and interact with whole-slide images in .svs format using the OpenSlide python library. Using Flask and the provided web based viewer example, I am able to create a web based application that allows me to…
ceso
  • 101
  • 1
  • 6
4
votes
1 answer

No module named 'openslide'

I created a virtual environment with conda, and installed open slide. I activated my environment, but when I try to run my Python script, I get an error saying: import openslide ModuleNotFoundError: No module named 'openslide' I'm using python3. …
user5161995
4
votes
1 answer

Openslide-python import error

I receive the following error when running import openslide from inside python terminal Traceback (most recent call last): File "", line 1, in File "C:\dev_res\python\python2_713\lib\site-packages\openslide\__init__.py",…
user3763012
  • 171
  • 1
  • 1
  • 10
3
votes
0 answers

Openslide: Remove “label” image for Philips TIFF files

I'm using openslide-python to read whole slide images in the Philips format. I am trying to anonymize the data by removing the label associated image by deleting/replacing this: slide.associated_images["label"] However it raises: TypeError:…
Vendetaheist23
  • 41
  • 4
3
votes
1 answer

How to resolve "OpenSlideUnsupportedFormatError"?

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 =…
Sahithi
  • 31
  • 2
3
votes
2 answers

ImportError: Couldn't locate OpenSlide dylib. Is OpenSlide installed?

Context Issue type : import error Operating system : Mac OS 10.14.5 OpenSlide Python version : openslide-python 1.1.1 Details hi, I have installed openslide-python 1.1.1 on Mac OS 10.14.5 (in a virtualenv environment) with the command : pip…
clems
  • 129
  • 2
  • 8
3
votes
0 answers

OpenSlide-python install in windows10

Plateform: win10 home Python 3.7.2 (tags/v3.7.2:9a3ffc0492, Dec 23 2018, 22:20:52) [MSC v.1916 32 bit (Intel)] on win32 I want to run deepzoom sample in windows 10. follow the:https://github.com/openslide/openslide-python#installation 1. Install…
Kamil
  • 594
  • 1
  • 8
  • 28
2
votes
1 answer

Opening pyramidal images ob google collab: large_image getTileSource doesn't work on google collab (No available tilesource for ndpi)

I used all of these commands to make sure I have everything that's needed for loading dpi pyramidal images on google collab with no luck so far. !pip install large_image !apt update && apt install -y openslide-tools !pip install…
AMM
  • 2,195
  • 2
  • 20
  • 28
2
votes
1 answer

Is it possible to use OpenSlide on Google Colab?

I need to split a tif image in patches. Images are in a gigapixel resolution and it takes really long on my machine. Is it possible to use OpenSlide on Google Collaboratory?
vftw
  • 1,547
  • 3
  • 22
  • 51
2
votes
1 answer

openslide python import show:windows error

I am using python 2.7 win 32 I need to install openslide in python in below page show Install openslide http://openslide.org/download/ which item download for windows. i tried every thing.and pip installation the error shows below import…
Anas Mubarak
  • 21
  • 1
  • 3
1
2 3 4