diff --git a/README.md b/README.md index fd131ca..4f4f8f4 100644 --- a/README.md +++ b/README.md @@ -4,38 +4,13 @@ ![CI](https://github.com/angelolab/Nimbus-Inference/actions/workflows/ci.yaml/badge.svg) [![Documentation Status](https://readthedocs.org/projects/nimbus-inference/badge/?version=latest)](https://nimbus-inference.readthedocs.io/en/latest/?badge=latest) - +[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1mLt2K9_rqUhr3Z4CLw_znS12KSUVSPzj?usp=sharing) The Nimbus repo contains code for inference of a machine learning model that classifies cells into marker positive/negative for arbitrary protein markers and different imaging platforms. ## Installation instructions -Clone the repository - -`git clone https://github.com/angelolab/Nimbus-Inference` - - -Make a conda environment for Nimbus and activate it - -`conda create -n Nimbus python==3.10` - -`conda activate Nimbus` - -Install CUDA libraries if you have a NVIDIA GPU available - -`conda install -c conda-forge cudatoolkit=11.8 cudnn=8.2.0` - -Install the package and all depedencies in the conda environment - -`python -m pip install -e Nimbus-Inference` - - -Navigate to the example notebooks and start jupyter - -`cd Nimbus-Inference/templates` - -`jupyter notebook` - +Create an environment with a Python version between 3.9-3.11 and install this package via `pip install Nimbus-Inference`, then download the template notebook from here [1_Nimbus_Predict.ipynb](https://github.com/angelolab/Nimbus-Inference/blob/main/templates/1_Nimbus_Predict.ipynb) to get started. ## Release notes