Environment

Check the nvidia installation by running: nvidia-smi and nvcc --version

Install

First time running:

git clone https://github.com/2454511550Lin/octopi-malaria-gui.git
cd octopi-malaria-gui
python3 run.py

If no error occurs, one can create desktop shortcut

bash create_shortcut.sh

Now the desktop has a octopi malaria icon, one should right click and select "Allow Lunching". Then one can double click the icon to lunch the program.

Google Cloud Storage

Optionally, one can use Google Cloud Storage to store the data. The configuration is as follows:

pip install google-cloud-storage

Then one can configure the bucket name and the path to the service account json key as:

echo 'export BUCKET_NAME="your_bucket_name"' >> ~/.bashrc
echo 'export SERVICE_ACCOUNT_JSON_KEY="path_to_your_service_account_json_key"' >> ~/.bashrc

Only for new computer and environment

Please refer to Cephla's forum to install Ubuntu 20.04.6.

Software

wget https://raw.githubusercontent.com/hongquanli/octopi-research/master/software/setup_22.04.sh
chmod +x setup_22.04.sh
./setup_22.04.sh

SciPy has to be 1.12.0, otherwise spot detection could have some issues. Which can be installed by pip install scipy==1.12.0

CUDA / Driver

wget https://raw.githubusercontent.com/hongquanli/octopi-research/master/software/setup_cuda_22.04.sh
chmod +x setup_cuda_22.04.sh
./setup_cuda_22.04.sh