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Questions tagged [openslide]

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

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53 questions
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is it possible to create SVS files at all?

I read a lot of resources saying that creating svs files is impossible. Is there any way to tweak the tif file contents in such a way that it can be saved as a SVS file by any chance. I was able to create a Aperio Tif slide using this tutorial. Can…
major
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Converting png / jpg images to svs / tif image format

How can I convert png or jpg image files to svs or tif Aperio image formats? It can be in python, c++, c# or java. Is there any library that support tif or svs format?
Melody
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How to use OpenSeaDragon with Virutal Slide

I am new to openseadragon and would like to create a webbased viewer from some Aperio .svs while slide images. I am using c# and .net and have openslide creating thumbnails, barcode images, etc. But I am stuck on how do to get openseadragon to…
jdogitt
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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 python scripting, c## as well as the one in php:…
Ahamed Husain
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Color noise removal from whole slide image patch

Afternoon, I am doing some deep learning with whole slide images (biomedical images of physical samples). Im using openslide to tile up the whole slide image (5gb in size) into smaller patches of the whole image and then convert this to RGB color…
maracuja
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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: https://github.com/openslide/openslide-python/tree/master/examples/deepzoom . I need…
Dmytro Ohorodnik
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Openslide read_region gives integer overflow

I am trying to read an image blob, with read size greater than 32767, 32767. I am am getting an error of integer overflow. Can somebody tell me as what is the maximum size I can read into?
Vaibhav Khanduja
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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. After this operation, 44.7 MB of additional disk…
Ramkumar Hariharan
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How to convert .ndpi and .vms files into dzi

I have a problem with the openseadragon. I cant convert the ndpi file into deep zoom image(dzi) and it cant directly open the ndpi image. $file_name = '22R23003.ndpi'; $file = '22R23003'; $converter = new…
Haseeb hanif
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I'm working on openslide for wholeslide images of .svs file i try to run the code getting memory error

working on openslide wholeslide images of .svs data it was a big set of data loaded in machine and working fine upto 50% and getting memory error, My machine is 64bit 16gb ram i tired to resize the .svs file, need to know how to resize and solve…
Çhârlïé
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How to display specific IFD of a TIFF file using Python

I have a tiff file with several Image File Directories (IFD). I would like to use Python to specifically display the image associated with an IFD. I know I can use tools such as tiffdump of tiffinfo to display all the relevant metadata for each IFD.…
gota
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Python: display the images contained in the different directories inside a TIFF image

How can I display the image (pixel data) of the different directories inside a single tiff file? I have several tiff-based files (of format ndpi, svs, bif, etc these are digital pathology images) each of which contain a pyramidal-like structure of…
gota
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I want to use the openslide functionality in pyvips

I tried to use both openslide and pyvips and my application doesn't find the necesary .dll. I think it is a problem of using both librarys. I have read that pyvips has openslide embed but I can't find how to use it. The main purpose for this is to…
Seakz
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Questions about openslide image processing operations

I am now using C++ to study related operations on pathological images, which involves the openslide library. I try to use the openslide_read_region(openslide_t* osr, uint32_t* dest, int64_t x, int64_t y, int32_t level, int64_t w, int64_t h);…
Xifeng
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How to convert an part of Tiff file image read by read_region to again Openslide object

I'm reading a tiff file using OpenSlide. Due to its large size, I'm planning to read the image by regions of 4k x 4k using read_region() function. After getting that region, I want to do the same process I have planned for the complete tiff file. To…
SjAnupa
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