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