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# Universal Cell Embeddings - Demo Instructions
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## Overview
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This demo allows users to upload a `.h5ad` file and process it using a pre-trained Universal Cell Embedding (UCE) model. The demo has two primary functionalities:
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1. **Generate Embeddings**: Upload a `.h5ad` file, and the model will output the embeddings for the loaded cells.
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2. **Cell-Type Classification**: For cells from the Tabula Sapiens v1 dataset, users can further classify the cell types based on the embeddings.
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## Features
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- **Upload and Embedding Generation**: Upload your `.h5ad` file containing single-cell RNA sequencing data, and the UCE model will generate embeddings representing the cells.
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- **Human Cell-Type Classification**: Specifically for human data from the Tabula Sapiens v1 dataset, the demo can classify cells into known cell types based on the generated embeddings.
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## How to Use the Demo
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1. **Upload a `.h5ad` File**:
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- Click on the "Upload File" button.
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- Select your `.h5ad` file from your device. Ensure that the file is formatted correctly.
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2. **Generate Embeddings**:
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- After the file is uploaded, click on the "Generate Embeddings" button.
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- The model will process the data and output the embeddings for each cell.
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3. **Cell-Type Classification (Optional)**:
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- If your data comes from the Tabula Sapiens v1 dataset, you can click on the "Classify Cell Types" button after generating embeddings.
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- The demo will output the predicted cell types based on the embeddings.
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## Supported Data
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- **Input Format**: The demo accepts `.h5ad` files.
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- **Supported Dataset**: The classification functionality is tailored for human data from Tabula Sapiens v1. Other datasets will only generate embeddings without classification.
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## Example Workflow
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1. **Step 1**: Upload your `.h5ad` file.
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2. **Step 2**: Click "Generate Embeddings" to get the cell embeddings.
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3. **Step 3**: (Optional) If working with Tabula Sapiens v1, click "Classify Cell Types" for classification results.
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## Future Enhancements
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- Expanding the classification functionality to support more datasets and species.
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- Providing visualization tools for the embeddings directly within the demo.
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## Limitations
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- The classification feature is limited to Tabula Sapiens v1 dataset.
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- For other datasets, only the embeddings will be generated without classification.
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## Contact and Feedback
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For any issues or feedback, please contact the development team through the Hugging Face community or open an issue in the repository.
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