File size: 2,514 Bytes
45f0e71 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 |
# 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.
|