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INSTALL.md

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MESCnn Installation

We tested the following instructions to install all the dependencies required to run the MESCnn pipeline on Ubuntu 20.04. Please note that it should work fine also on other operating systems. Though, some Python dependencies, like Detectron2, may be more difficult to set-up on a Windows system.

System Dependencies

The following system dependencies are required:

  1. Install Java Runtime Environment (JRE) and Java Development Kit (JDK):
sudo apt install default-jdk
sudo apt install default-jre
  1. Install Openslide:
sudo apt-get install openslide-tools
  1. Download and install QuPath.

Python Dependencies

You may want to have the Python dependencies installed inside a virtual environment. We recommend the adoption of Anaconda, since we used it in all our experiments.

As first thing, you should create and activate an Anaconda virtual environment, please note that we used Python 3.7 throughout our tests:

conda create --name MESCnn-Env python=3.7
conda activate MESCnn-Env

Then, you need to install the required Python packages. Due to a problem in functools, we suggest to install first the two following packages:

pip install numpy cached-property

Then, install PyTorch with CUDA support:

pip install torch==1.13.1 torchvision==0.14.1 --index-url https://download.pytorch.org/whl/cu117

Lastly, install all the other requirements:

pip install -r requirements.txt

At this point, install Detectron2:

python -m pip install 'git+https://github.com/facebookresearch/detectron2.git'

To solve the aforementioned problem in functools, edit the file detectron2/utils/events.py of the installed Detectron2 library, by replacing from functools import cached_property with from cached_property import cached_property.

Notes

  • If Paquo cannot find the QuPath directory, you may need to add a .paquo.toml file, as reported by Paquo documentation. In this case, create such file in the root directory of the MESCnn cloned repository, and put the following lines, setting the qupath_dir as appropriate:
qupath_dir="path/to/your/qupath/installation"
MOCK_BACKEND=false
  • If some local modules are not found and the pipeline raise the ModuleNotFoundError for those modules, add the root directory of the project to the Python path:
export PYTHONPATH=.
  • If you get the following error: OSError: /lib/x86_64-linux-gnu/libgobject-2.0.so.0: undefined symbol: ffi_type_uint32, version LIBFFI_BASE_7., try to run the following line in terminal:
export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libffi.so.7