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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/EliHei2/segger_dev/main.svg)](https://results.pre-commit.ci/latest/github/EliHei2/segger_dev/main)
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**Important note (Dec 2024)**: As segger is currently undergoing constant development we highly recommending installing segger directly via github.
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**segger** is a cutting-edge tool for **cell segmentation** in **single-molecule spatial omics** datasets. By leveraging **graph neural networks (GNNs)** and heterogeneous graphs, segger offers unmatched accuracy and scalability.
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# How segger Works
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## Installation Options
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## Installation
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**Important note (Dec 2024)**: As segger is currently undergoing constant development we highly recommending installing segger directly via github.
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### Important: PyTorch Geometric Dependencies
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Afterwards choose the installation method that best suits your needs.
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### Micromamba Installation
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To set up Segger with `micromamba` and install the required dependencies, use the following commands:
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```bash
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micromamba create -n segger-rapids --channel-priority 1 \
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-c rapidsai -c conda-forge -c nvidia -c pytorch -c pyg \
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rapids=24.08 python=3.* 'cuda-version>=11.4,<=11.8' jupyterlab \
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'pytorch=*=*cuda*' 'pyg=*=*cu118' pyg-lib pytorch-sparse
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micromamba install -n segger-rapids --channel-priority 1 --file mamba_environment.yml
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micromamba run -n segger-rapids pip install --no-deps ./
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```
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### GitHub Installation
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For a straightforward local installation from GitHub, clone the repository and install the package using `pip`:
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```bash
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git clone https://github.com/EliHei2/segger_dev.git
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cd segger_dev
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pip install -e "."
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```
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#### Pip Installation (RAPIDS and CUDA 11)
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For installations requiring RAPIDS and CUDA 11 support, run:

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