| --- |
| license: other |
| license_name: modified-apache-2.0-noncommercial |
| license_link: LICENSE |
| extra_gated_heading: "Acknowledge license terms: non-commercial use" |
| extra_gated_button_content: "I agree to the license terms" |
| --- |
| |
| # deepcell-types |
|
|
| DeepCell Types is a novel approach to cell phenotyping for spatial proteomics |
| that addresses the challenge of generalization across diverse datasets with |
| varying marker panels. |
|
|
| See the [deepcell-types paper][paper] for details! |
|
|
| [paper]: https://www.biorxiv.org/content/10.1101/2024.11.02.621624v3.full |
|
|
| ## Model Details |
|
|
| deepcell-types is a language-informed vision model comprising three main |
| components: |
|
|
| 1. A visual encoder, |
| 2. A language encoder, and |
| 3. A channel-wise transformer. |
|
|
| See the [deepcell-types paper][paper] for further details. |
|
|
| ### Model Description |
|
|
| - **Developed by:** Van Valen Lab |
| - **Funded by:** [Funding details](https://www.biorxiv.org/content/10.1101/2024.11.02.621624v3.full#sec-16) |
| - **Model type:** Language-informed vision model |
| - **License:** Modified-apache2.0-noncommercial |
|
|
| ### Model Sources [optional] |
|
|
| - **Repository:** https://github.com/vanvalenlab/deepcell-types |
| - **Paper [optional]:** https://www.biorxiv.org/content/10.1101/2024.11.02.621624v3.full |
| - **Demo [optional]:** https://vanvalenlab.github.io/deepcell-types/site/tutorial.html |
|
|
| ## Uses |
|
|
| Cell phenotyping for spatial proteomic images. |
|
|
| ### Direct Use |
|
|
| The weights provided in this repository are suitable for cell phenotype prediction |
| across a variety of tissues and spatial proteomic imaging methods. |
|
|
| ### Downstream Use |
|
|
| deepcell-types is a generalist model designed to perform cell-type prediction |
| across all cell types and spatial proteomic imaging modalities. |
| However, it is possible to fine-tune deepcell-types for specific applications. |
| See the [methods section of the paper][fine-tuning] for details. |
|
|
| [fine-tuning]: https://www.biorxiv.org/content/10.1101/2024.11.02.621624v3.full#sec-14 |
|
|
| ### Out-of-Scope Use |
|
|
| **The model herein is provided subject to license terms prohibiting use for |
| commercial applications.** |
|
|
| Inquiries regarding commercial licensing should be directed to the |
| [Caltech Office of Technology Transfer][ottcp]. |
|
|
| [ottcp]: https://innovation.caltech.edu/about-ottcp/contact-us#send-us-a-message |
|
|
| ## How to Get Started with the Model |
|
|
| See the [`deepcell-types` tutorial][tutorial]. |
|
|
| [tutorial]: https://vanvalenlab.github.io/deepcell-types/site/tutorial.html# |
|
|
