This repository contains code for the automatic detection of Nuclear Pore Complexes (NPC) in localization microscopy. Developed as part of the AI4Life project, it uses data provided by Emilie Costes from the CBS, Montpellier, FR. All images used in this tutorial are licensed under CC-BY. If any of the instructions are not working, please open an issue or contact us at ai4life@fht.org!
The project focuses on ...
Install the conda package, dependency and environment manager.
You can download this repository from the green Code button → download ZIP, or clone through the command line with
cd <path to any folder of choice>
git clone https://github.com/BIIFSweden/AI4Life_OC3_18.git
Then create the AI4Life_OC3_18 conda environment:
cd <path to your 'AI4Life_OC3_18' directory>
conda env create -f environment.yml
This will install all necessary project dependencies.
Copy all project data to the data directory (or use symbolic links).
Then run Jupyter Lab from within the AI4Life_OC3_18 conda environment:
cd <path to your 'AI4Life_OC3_18' directory>
conda activate AI4Life_OC3_18
jupyter-lab
Inside the notebooks folder you will find Jupyter notebooks for:
AI4Life has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101057970. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.
Developed by Kristina Lidayova