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JLrumberger authored Sep 25, 2024
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![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

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