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ericup committed Aug 26, 2023
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# Cell Detection

[![Downloads](https://pepy.tech/badge/celldetection?l)](https://pepy.tech/project/celldetection)
[![Downloads](https://static.pepy.tech/badge/celldetection?l)](https://pepy.tech/project/celldetection)
[![Test](https://github.com/FZJ-INM1-BDA/celldetection/workflows/Test/badge.svg)](https://github.com/FZJ-INM1-BDA/celldetection/actions?query=workflow%3ATest)
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</details>

## 🐳 Docker

Find us on Docker Hub: https://hub.docker.com/r/ericup/celldetection

You can pull the latest version of `celldetection` via:
```
docker pull ericup/celldetection:latest
```

<details>
<summary style="font-weight: bold; color: #888888">CPN inference via Docker with GPU</summary>

```
docker run --rm \
-v $PWD/docker/outputs:/outputs/ \
-v $PWD/docker/inputs/:/inputs/ \
-v $PWD/docker/models/:/models/ \
--gpus="device=0" \
celldetection:latest /bin/bash -c \
"python cpn_inference.py --tile_size=1024 --stride=768 --precision=32-true"
```
</details>
<details>
<summary style="font-weight: bold; color: #888888">CPN inference via Docker with CPU</summary>

```
docker run --rm \
-v $PWD/docker/outputs:/outputs/ \
-v $PWD/docker/inputs/:/inputs/ \
-v $PWD/docker/models/:/models/ \
celldetection:latest /bin/bash -c \
"python cpn_inference.py --tile_size=1024 --stride=768 --precision=32-true --accelerator=cpu"
```
</details>



### Apptainer

You can also pull our Docker images for the use with [Apptainer](https://apptainer.org/) (formerly [Singularity](https://github.com/apptainer/singularity)) with this command:

```
apptainer pull --dir . --disable-cache docker://ericup/celldetection:latest
```


## 🤗 Hugging Face Spaces

Find us on Hugging Face and upload your own images for segmentation: https://huggingface.co/spaces/ericup/celldetection
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