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README.md

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## Installation
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You need to install [PyTorch](https://pytorch.org/get-started/locally/), [SegmentAnything](https://github.com/facebookresearch/segment-anything#installation), [napari](https://napari.org/stable/) and [elf](https://github.com/constantinpape/elf).
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We require these dependencies:
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- [PyTorch](https://pytorch.org/get-started/locally/)
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- [SegmentAnything](https://github.com/facebookresearch/segment-anything#installation)
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- [napari](https://napari.org/stable/)
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- [elf](https://github.com/constantinpape/elf)
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We recommend to use conda and provide two conda environment files with all necessary requirements:
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- `environment_gpu.yaml`: sets up an environment with GPU support.
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- `environment_cpu.yaml`: sets up an environment with CPU support.
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You can create the corresponding environment via
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To install via conda first clone this repository:
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```
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git clone https://github.com/computational-cell-analytics/micro-sam
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```
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and
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```
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cd micro_sam
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```
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Then create either the GPU or CPU environment via
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```
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conda env create -f <ENV_FILE>.yaml
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```
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You can then activate the environment via
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Then activate the environment via
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```
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conda activate sam
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```

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