slideNormalize

slideNormalize: normalisation of histological high-resolution images.

We have tested slideNormalize on CentOS7 and macOS Mojave+ (version 10.14.5+).

Please tell us if you run into problems, it is likely we can help you out - we have done this before. ;)

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Installation

Download and install the latest version of the slideNormalize from GitHub. First create and go to the git directory, then download slideNormalize.

mkdir -p ~/git/ && cd ~/git

if [ -d ~/git/slideNormalize/.git ]; then \
		cd ~/git/slideNormalize && git pull; \
	else \
		cd ~/git/ && git clone https://github.com/swvanderlaan/slideNormalize.git; \
	fi

Binaries

For your convenience, we have created precompiled binaries for CentOS7+ and macOS Mojave (10.14.5+) using g++, c++11 and opencv. These are available in the binaries folder:

• slideNormalize_macOS_Mojave10145
• slideNormalize_macOS_BigSur1152
• slideNormalize_centos7

Compile from source

slideNormalize requires opencv which you can install via brew.

brew install opencv

It will probably be keg-only, so you need to make sure that opencv is in your $PKG_CONFIG. Add this to your .bashrc or .bash_profile

### For OPENCV
# For slideNormalize -- brew install opencv
# If you need to have opencv first in your PATH run:
export PATH="/usr/local/opt/opencv/bin:$PATH"

# For compilers to find opencv you may need to set:
export LDFLAGS="-L/usr/local/opt/opencv/lib"
export CPPFLAGS="-I/usr/local/opt/opencv/include"

# For pkg-config to find opencv you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/opencv/lib/pkgconfig"

Because the compiler expects opencv.pc you also need to link opencv4.pc to this:

ln -sv /usr/local/opt/opencv/lib/pkgconfig/opencv4.pc /usr/local/opt/opencv/lib/pkgconfig/opencv.pc

Finally, as slideNormalize uses tclap, you'll need to install this too.

 brew install tclap

slideNormalize in your path

You can add slideNormalize to your path by running the code below to make a symbolic link, while making sure to choose the binary appropriate for you system (macOS or CentOS).

mkdir -pv ~/bin/ && \
	ln -s -f -v ~/git/slideNormalize/binaries/slideNormalize_mac ~/bin/slideNormalize

Example usage

The program uses the TCLAP library for command-line argument parsing. Here is the list of command-line arguments:

Argument(s):

• -f or --file
  • The filename of the NDPI/TIF file to process. (Example: -f input_image.tif)

Optional argument(s):

• -o or --output
  • The output filename of the NDPI/TIF file to process. If not provided, a default filename will be generated based on the input filename. (Example: -o output_image.tif)
• -e or --extension
  • The standard output filename extension of the image-tile to process. If provided, it will be used in the generated output filename. (Example: -e normalized)
• -s or --show
  • Show results in a graphical interface. This is a switch, and if included, it will trigger the display of results. (Example: -s)

Here's an example of how you might run the program from the command line:

./slideNormalize -f input_image.tif -o output_image.tif -e normalized -s

The -f flag specifies the input file, -o specifies the output file, -e specifies the extension, and -s triggers the graphical display of results.

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Licence

The MIT License (MIT): http://opensource.org/licenses/MIT.

Copyright (c) 2017-2024, Tim Bezemer & Sander W. van der Laan, UMC Utrecht, Utrecht, the Netherlands.