openslide | C library for reading virtual slide images | Computer Vision library

by openslide C Version: v3.4.1 License: LGPL-2.1

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | openslide Summary

openslide is a C library typically used in Artificial Intelligence, Computer Vision, Tensorflow applications. openslide has no bugs, it has no vulnerabilities, it has a Weak Copyleft License and it has low support. You can download it from GitHub.

Carnegie Mellon University and others.

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Quality

Security

License

Reuse

Support

openslide has a low active ecosystem.

It has 332 star(s) with 193 fork(s). There are 33 watchers for this library.

It had no major release in the last 12 months.

There are 96 open issues and 227 have been closed. On average issues are closed in 523 days. There are 22 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of openslide is v3.4.1

Quality

openslide has 0 bugs and 29 code smells.

Security

openslide has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

openslide code analysis shows 0 unresolved vulnerabilities.

There are 1 security hotspots that need review.

License

openslide is licensed under the LGPL-2.1 License. This license is Weak Copyleft.

Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

Reuse

openslide releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

It has 837 lines of code, 44 functions and 13 files.

It has medium code complexity. Code complexity directly impacts maintainability of the code.

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openslide Key Features

No Key Features are available at this moment for openslide.

openslide Examples and Code Snippets

No Code Snippets are available at this moment for openslide.

Community Discussions

Trending Discussions on openslide

How to scale up the 20x (.svs whole-slide-image) to 40x slides?

How to export and migrate OpenSlides database?

Manual Annotation with Tkinter

How to merge tiles obtained using openslide-python

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

QUESTION

How to scale up the 20x (.svs whole-slide-image) to 40x slides?

Asked 2021-Aug-18 at 11:10

I have a whole-slide-images (.svs format) which are scanned at 20x. For my problem, I would like to upscale the slides to 40x along with the slide metadata. I tried it by the combination of the openslide, NumPy, cv2, and vips command. For a smaller size of slides, I can achieve this but for larger size slides I can't. Is there a straightforward way available to achieve this?

I followed following steps

open slide and NumPy to read the slide.
cv2 to create the png upscaled .png image.
vips vips2tiff command to convert .png to .svs file.

...

ANSWER

Answered 2021-Aug-18 at 11:10

I would just use libvips resize. For example:

Source https://stackoverflow.com/questions/68830623

QUESTION

How to export and migrate OpenSlides database?

Asked 2021-Apr-12 at 12:03

I encountered an error message while exporting my OpenSlides database. My goal is to switch from a SQLite database to PostgreSQL database in OpenSlides, but unfortunately, as I said, exporting doesn't quite work.

Can someone help me please?

Error Message:

ModuleNotFoundError: No module named 'settings'

...

ANSWER

Answered 2021-Apr-12 at 12:03

Found the solution. You have to enter openslides createsettings so that the settings file is created first. Then it can find the settings.py

Source https://stackoverflow.com/questions/67057418

QUESTION

Manual Annotation with Tkinter

Asked 2021-Feb-01 at 21:51

I am using Tkinter to import images with Openslide. I would like to integrate a manual annotation module into my program like this:

...

ANSWER

Answered 2021-Jan-05 at 14:46

So if I got it right from the comments, the issue is to be able to both pan the slide and draw on it using binding to mouse clicks and motion. There are several way to do that, for instance:

Use radiobuttons so that the user selects the "mode": either pan or annotate. Here is a small example based on https://stackoverflow.com/a/50129744/6415268 for the drawing part. The click() and drag() functions do different actions depending on the selected mode (stored a the StringVar).

Source https://stackoverflow.com/questions/65575880

QUESTION

How to merge tiles obtained using openslide-python

Asked 2021-Jan-11 at 17:14

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:

...

ANSWER

Answered 2021-Jan-11 at 17:14

libvips can do this merge and join for you. You can call it from pyvips, the Python binding.

To load an svs image and split it into tiles you can write:

Source https://stackoverflow.com/questions/65661572

QUESTION

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

Asked 2020-Aug-15 at 12:34

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 then nothing happens: there is no output, no error message and the SLURM job keeps running.

I assume the entire contents of the python script are not relevant (but I included it anyway for completion). For debugging purposes I inserted the print("script started") line at the very beginning to see if it gets run but it doesn't. The last thing I see in the output is moved to directory.

I tried calling a test.py script containing print("test")right before this and it gets executed normally.

What could be the reason the python script doesn't start and how can I fix it?

Edit: As user jakub recommended changing print("script started")to print("script started", flush=True)successfully gets printed. Including several more of these statements revealed that the script was actually running perfectly fine, it just didn't output anything. Including the same statement within the for loop that gets constantly executed also makes all print() statements previously missing get printed.

The question then turns into: why do the print() statements here need to have flush=True in this script but not in other scripts?

Shell script:

...

ANSWER

Answered 2020-Aug-15 at 12:34

Python buffers stdin, stdout, and stderr by default. print() writes to stdout by default, so you will see this buffered behavior.

From https://stackoverflow.com/a/14258511/5666087 :

Python opens the stdin, -out and -error streams in a buffered mode; it'll read or write in larger chunks, keeping data in memory until a threshold is reached.

You can forcibly flush this buffer by passing flush=True to print. See the documentation for more information. If you have multiple print statements in a row, you need only use flush=True in the last one.

Source https://stackoverflow.com/questions/63414318

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install openslide

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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