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NoraKrbr merged 2 commits into from
Aug 25, 2026
Merged

Repo check #49

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updated installation and dataloader information
NoraKrbr Aug 25, 2026
e988127
Merge pull request #48 from Kainmueller-Lab/main
NoraKrbr Aug 25, 2026
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18 changes: 10 additions & 8 deletions README.md
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Expand Up @@ -11,8 +11,16 @@ Assumes a .env file with the following variables:
- `HF_TOKEN`: Huggingface API token to download models with access restrictions

## Installation
install the environment with:
`conda env create -f env.yaml`
install the project with:
```conda create -n <myenv> python=3.10 pip
conda activate <myenv>
pip install -e .```

## Data
The data can be downloaded via huggingface:
https://huggingface.co/datasets/Kainmueller-Lab/phenobench

The dataloaders can be found in the following repository, which is already included in this repository as a dependency: https://github.com/Kainmueller-Lab/Bio-Image-Datasets

## GPU requirements

Expand All @@ -21,12 +29,6 @@ This project is designed to run training and large-model evaluation on NVIDIA GP
- **CUDA / PyTorch**: Built and tested with CUDA 11.8-compatible PyTorch (see `pyproject.toml` supplemental wheel for `cu118`). Install a PyTorch build that matches your system's CUDA runtime (CUDA 11.8 recommended).
- **NVIDIA drivers & libraries**: NVIDIA driver compatible with CUDA 11.8, cuDNN and NCCL installed on the system (or available via container image).

## Data
The data can be downloaded via huggingface:
https://huggingface.co/datasets/Kainmueller-Lab/phenobench

The dataloaders can be found in the following repository: https://github.com/Kainmueller-Lab/Bio-Image-Datasets

## Running the Benchmark
Once you have downloaded the dataset, and installed the required packages, the code can be run with the following command:

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