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
0
votes
0 answers

Google Colab Pro runs out of ram(35GB) while reading a WSI tiff file using Open Slide

I'm trying to pre-process WSI images using PyTorch. I have stored the WSI images in google drive and mounted it to my google colab pro account(which is having 35GB ram) and trying to read them. To read the images, I'm using openslides. Images were…
SjAnupa
  • 102
  • 10
0
votes
1 answer

Trouble importing Openslide

I am trying to import openslide in a jupyter notebook, but I am repeatedly getting this error. I am getting the same error when I try to import by running python in terminal also. ImportError: Couldn't locate OpenSlide dylib. Is OpenSlide…
Sam
  • 1
0
votes
1 answer

How show Whole-slide image (.svs) in PySide2

I want to use pyside2 to develop a pathological image recognition tool, but I don't know how to display the whole slide image (the suffix is .svs), just like the function of ASAP software can quickly open and display images.
coding
  • 1
0
votes
1 answer

Reading and resizing svs slide results in a damaged image

I'm using OpenSlide and PIL to open slides and resize them. For some of the slides, the resulting images are partly black. To reproduce the error, use this slide and this script: def slide_to_scaled_pil_image(slide, SCALE_FACTOR=32): """ Convert…
Some student
  • 131
  • 2
  • 13
0
votes
0 answers

Issue with using OpenSlide

I am new to C# and can't get OpenSlide to work. I need it to be able to read SVS files. Below is the code I have used. Is it possible I am missing something in a directory? My boss has used the same code and can get it to run without issue. I am…
Stuart
  • 21
  • 1
0
votes
1 answer

how to convert dzi files to multi-tile pyramidal tiff format

In reference to the answer (how to convert dzi (deep zoom) files to full image) I am a noob on this topic, please correct if I am wrong. I am trying to create a multi-tiled tiff from .dzi (deep zoom image) format, how I am doing is: (i) Pick the…
Harish Kumar Thirugnanam
  • 13
  • 1
  • 6
0
votes
1 answer

How to make "Openseadragon" prioritize tile requests?

I am using Openseadragon to show Whole Slide Images running on a server. When internet connection is not very fast and navigating inside the image, I have many requests pending on the queue that needs to be finished until the specific area I want to…
CRISPR
  • 891
  • 1
  • 6
  • 6
0
votes
1 answer

Pip install openslide completes successfully but when I import it "the specified module is not found"

I need to open SVS images in Python 3.7 and it seems that Openslide is the only module capable of opening images of that size (30k*30k pixels). I have used pip install openslide-python as well as python -m pip install openslide-python and pip 3…
Kyle Brim
  • 11
  • 2
0
votes
0 answers

how to solve the ddl and libraray path problem in python with module not found

i want to use openslide library in code , installed it but in jupyter notebook ,it is giving error for module not found..: when import openslide it gives the following error: C:\ProgramData\Anaconda3\lib\site-packages\openslide\__init__.py in…
sheprogrm
  • 1
  • 1
0
votes
1 answer

Install openslide and its dependency openjpeg on ubuntu without root privileges

I am connected to a server via ssh and do not have root privileges. I ultimately need to install openslide. apt-get is not present, yum requires root privilege so I was going for make/install from the source code of openslide. I needed to install…
Uğur Dinç
  • 303
  • 3
  • 16
0
votes
0 answers

anonymize-slide problem with creating object

I am trying to update anonymize slide (which deletes slide labels from scanned virtual slides) to work with Python3. It was written for Python2.6 or 2.7. I don't think that python version compatibility is the problem here, though I could be wrong.…
LobstaBoy
  • 515
  • 1
  • 3
  • 10
0
votes
1 answer

Openslide won't show the mmpx property for level_count-1

The property "openslide.mmp-x" shows the property containing the number of microns per pixel in the X dimension of level 0. As I am showing the level_count-1 I don't want the property for level 0 but for level_count-1. How do I get that property of…
jadem
  • 27
  • 4
0
votes
1 answer

got an error on decoding jpeg2000 in c++ with OpenJPEG

I am trying to decode JPEG2000 format with OpenJPEG. (Decoding just one raw tile buffer from a svs file.) But I got an error on opj_read_header(). Is there something I forgot to set before calling opj_read_header()? opj_image_t *image =…
YJJ
  • 45
  • 10
0
votes
1 answer

Convert image array to original svs format

I'm trying to apply a foreground extraction to a SVS image (Whole Slide Image) usign OpenSlide library. First, I converted my image to an array to work on my foreground extraction: image = np.asarray(oslIm.read_region((0, 0), level,…
vftw
  • 1,547
  • 3
  • 22
  • 51
0
votes
0 answers

Openslides on Ubuntu 18.04

I'm trying to install Openslide to visualize medical pictures. I have followed the simple instructions but I couldn't successfully start Openslide on my laptop. I used: pip install openslides but i get this error when i run "openslides" from my…
Andrea Grippi
  • 1,339
  • 4
  • 15
  • 27
1 2
3
4