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...

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...

Read region of a Large Width X Height Image

I have a 1gb image, I want to open this image into 90,000 and 70,000(width X height) at level 0. I even tried with python openslide but didn't work for me. Is there a way to do this ?

Cannot install openslide-python on google datalabs Jupyter notebook

I am trying to install openslide-python on google datalabs Jupyter notebook using: !apt-get install python-openslide It runs, until it prints out: Need to get 13.0 MB of archives. ...

Openslide-python import error

I receive the following error when running import openslide from inside python terminal <code>Traceback (most recent call last): File "<stdin>", line 1, in <module> File...

How do I understand the steps parameters in predict_generator?

I'm not so sure about the role of the steps parameter in predict_generator, and what I understand is that steps represents the amount of data generated by the generator, but someone denies my...

How to set PATH before imports occur in a nice way?

I have a Python script which uses openslide-python. openslide-python requires that OpenSlide binaries are in the DLL search path on Windows. I am planning to distribute my application in the...

Openslide: Replace "label" image

I'm using openslide-python to read whole slide images in the Mirax format (mrxs). Now I'd like to replace the "label" barcode image with a custom one. Unfortunately, f.associated_images["label"] =...

Processing very large images as numpy arrays

I am dealing with images greater than 8 GB in .svs format. Using openslide, I have read them as 1D numpy arrays. Now in order to feed them into an algorithm I need to reshape them into image form...

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...

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...

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...

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...

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...

IPC shared memory across Python scripts in separate Docker containers

The Problem I have written a neural network classifier that takes in massive images (~1-3 GB apiece), patches them up, and passes the patches through the network individually. Training was going...

How can I show openslide.deepzoom.DeepZoomGenerator in my PyQt5 interface?

I need to show openslide.deepzoom.DeepZoomGenerator in PyQt5. There are examples of showing DeepZoomGenerator in Flask web-interface. You can check them out here:...

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...

Error building a docker image gives an error: Failed to build wheel for pycurl(setup.py)

I am trying to create a docker image from a dockerfile but I keep encountering this error. ERROR: requests-oauthlib 1.2.0 has requirement oauthlib>=3.0.0, but you'll have oauthlib 2.1.0 which is...

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...

How to use Openslide-PHP-Bindings to create .dzi file

I'm trying to create .dzi file from a .svs file (downloaded from openslide.org test biomedical data). We found couple of libs including vips, php-vips and openslide's own lib openslide written in...

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...

Google Colaboratory gives me an error when I want to install OpenSlide

When I ran the following commands in the Jupiter notebook, it gives me an error. !apt-get install openslide-tools !pip install openslide-python ERROR: Command errored out with exit status 1:...

self._handle = _dlopen(self._name, mode) OSError: [WinError 126] The specified module could not be found

I am integrating geodjango in my real estate website, and I am tired of this error. Watching for file changes with StatReloader Exception in thread django-main-thread: Traceback (most recent call...

How to efficiently read part of a huge tiff image?

I have a collection of rather large tiff files (typical resolution is 30k x 30k to 50k x 50k). These have some interesting properties: 1. they contain several different resolutions of the same...

Larger than expected file sizes when saving a TIFF with OpenCV

I am creating a python program to load a .tiff image, crop out a selection from the image, and save the selection as a tiff. The dataset images are large, exceeding 1GB. I can successfully crop...

Errors when trying to use openslide and py_wsi

I'm trying to write a Python program to look at and hopefully edit svs files (add tags). I have pip installed openslide-python and py_wsi onto my computer, as well as installed OpenSlide and got a...

SLURM batch script doesn't execute Python script, returns no error message and doesn't stop running

In a SLURM cluster I am submitting a shell script that calls a python script (both scripts can be found below. When the shell script executes it get until where the python script is called but...

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...

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...

How to create patches of particular size at particular magnification of WSI slide?

I'm trying to create patches from a WSI slide (Available Here) at a particular magnification. I'm using OpenSlide in Python. I can convert the required magnification to particular level of slide...