# 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.