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README.md
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### Direct Use
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- Create biologically useful embeddings of microscopy images
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- Create contextualized embeddings of each channel of a microscopy image (set `return_channelwise_embeddings=True`)
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- Leverage the full MAE encoder + decoder to predict new channels / stains for images without all 6 CellPainting channels
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expected_output_dim = 384 * C if return_channelwise_embeddings else 384
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assert embeddings.shape == (2, expected_output_dim)
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```
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**Note: Currently, the model cannot be loaded via the `AutoModel` available in HuggingFace transformers library**
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### Direct Use
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+
- Create biologically useful embeddings of microscopy images
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- Create contextualized embeddings of each channel of a microscopy image (set `return_channelwise_embeddings=True`)
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- Leverage the full MAE encoder + decoder to predict new channels / stains for images without all 6 CellPainting channels
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expected_output_dim = 384 * C if return_channelwise_embeddings else 384
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assert embeddings.shape == (2, expected_output_dim)
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```
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We also provide a [notebook](https://huggingface.co/recursionpharma/OpenPhenom/blob/main/RxRx3-core_inference.ipynb) for running inference on [RxRx3-core](https://huggingface.co/datasets/recursionpharma/rxrx3-core).
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**Note: Currently, the model cannot be loaded via the `AutoModel` available in HuggingFace transformers library**
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