Cell detection using convolutional neural networks

Release contains files submitted as part of the bachelor's thesis

Instalation

1. clone this repo and cd to it

   git clone https://github.com/Ondrados/cnn-cells.git
   cd cnn-cells
   

2. create virtual enviroment and activate it

   virtualenv env
   source env/bin/activate
   

3. install dependencies

   pip install -r requirements_tiny.txt
   

4. download weights from releases and extract it inside cnn-cells folder

   wget https://github.com/Ondrados/cnn-cells/releases/download/v1.0/models.zip
   unzip models.zip -d models
   

5. export python path for this repository to your enviroment otherwise imports won't work

   export PYTHONPATH="${PYTHONPATH}:/path/to/cnn-cells"
   

6. run demo script which detect cells on 5 images

   python demo.py