Update README.md

README.md

@@ -1,5 +1,4 @@
 ---
-license: apache-2.0
 task_categories:
   - image-classification
   - feature-extraction
@@ -42,73 +41,10 @@ CT/
 └── 1.3.6.1.4.1.14519.5.2.1.6450.4007.2906.../ (104 slices)
 ```
 
-## Usage
-
-Install HoneyBee:
-
-```bash
-pip install honeybee-ml[all]
-```
-
-### Pathology — Load a whole-slide image
-
-```python
-from huggingface_hub import hf_hub_download
-from honeybee.loaders.Slide.slide import Slide
-from honeybee.processors.wsi import PatchExtractor
-
-slide_path = hf_hub_download(
-    repo_id="Lab-Rasool/honeybee-samples",
-    filename="sample.svs",
-    repo_type="dataset",
-)
-
-slide = Slide(slide_path)
-slide.detect_tissue(method="otsu")
-patches = PatchExtractor(patch_size=256).extract(slide)
-print(f"Extracted {len(patches)} patches from {slide.dimensions}")
-```
-
-### Clinical — Process a clinical PDF
-
-```python
-from huggingface_hub import hf_hub_download
-from honeybee.processors import ClinicalProcessor
-
-pdf_path = hf_hub_download(
-    repo_id="Lab-Rasool/honeybee-samples",
-    filename="sample.PDF",
-    repo_type="dataset",
-)
-
-processor = ClinicalProcessor()
-result = processor.process(pdf_path)
-print(result["entities"])
-```
-
-### Radiology — Download CT DICOM series
-
-```python
-from huggingface_hub import snapshot_download
-
-ct_dir = snapshot_download(
-    repo_id="Lab-Rasool/honeybee-samples",
-    repo_type="dataset",
-    allow_patterns="CT/**",
-)
-```
-
 ## Citation
 
 ```bibtex
-@article{rasool2024honeybee,
-  title={HoneyBee: A Scalable Modular Framework for Creating Multimodal Oncology Datasets with Foundational Embedding Models},
-  author={Rasool, Ghulam and others},
-  journal={arXiv preprint arXiv:2405.07460},
-  year={2024}
-}
-```
-
-## License
-
-Apache 2.0 — see the [HoneyBee repository](https://github.com/Lab-Rasool/HoneyBee) for details.
+Tripathi, A., Waqas, A., Schabath, M.B. et al. HONeYBEE: enabling scalable multimodal AI in
+oncology through foundation model-driven embeddings. npj Digit. Med. 8, 622 (2025).
+https://doi.org/10.1038/s41746-025-02003-4
+```