ST Tissue Recognition

November 29, 2017 ยท View on GitHub

st_tissue_recognition is a tool for creating masks around tissue sections in brightfield images. It uses the GrabCut algorithm, as implemented in OpenCV, along with a few tweaks to guess the initial segmentation of the image and to remove noise.

The library is written in C++. There is also a python extension that provides python bindings.

Dependencies

Main library

gcc 7+
CMake 3.8+
OpenCV 3.1.0+

Python module

In addition to the main library,

Python 2.7+ *or* Python 3.5+
numpy 1.11.1+
setuptools 20.1.1+

Python module example

In addition to the python module,

Pillow 4.1.0+
scipy 0.19.0+

Installation

Main library

  1. Install OpenCV.

  2. Run cmake on the root directory. For example,

    mkdir build
cd build
cmake ..
make install

Python module

  1. Install numpy and setuptools using your preferred package manager. For example, using pip:

    pip install numpy setuptools

  2. Run setup script:

    cd python-module
python setup.py install

Usage

Python module

See ./python-module/example.py for example usage.

Note: Remember to free the return values of get_binary_mask, downsample, and upsample using free.

Troubleshooting

Python module import error

OSError: libtissue-recognition.so: cannot open shared object file: No such file or directory.

The linker cannot find the object file of the library. Thus, you may need to add the dirname of the object file to the search path of the linker. If you configured the installation using cmake .., as in the installation instructions, the object file should be located in /usr/local/lib.

If you're using ld/GNU linker, you can try running

export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

and import the module again. To make the change permanent, either add the above command to the startup script of your shell (e.g., ~/.bashrc) or, perhaps better, add the library path to the ld config file:

[[ ! -e /etc/ld.so.conf.d/local.conf ]] && \
  echo "/usr/local/lib" | sudo tee /etc/ld.so.conf.d/local.conf >/dev/null && \
  sudo ldconfig