docs: update installation guide with SAM2 requirement

README.md

@@ -20,7 +20,11 @@ Segmentation model for whole-slide image (WSI) thumbnails, built on **Segment An
 Install dependencies:
 
 ```bash
+# Install AtlasPatch
 pip install atlas-patch
+
+# Install SAM2 (required for tissue segmentation)
+pip install git+https://github.com/facebookresearch/sam2.git
 ```
 
 Recommended: use the same components we ship in AtlasPatch. The segmentation service will (a) load your WSI with the registered backend, (b) build a 1.25× power thumbnail, (c) resize it to 1024×1024, (d) run SAM2 with a full-frame box, and (e) return a mask aligned to the thumbnail.
@@ -79,4 +83,14 @@ This model is released under **CC-BY-NC-SA-4.0**, which strictly disallows comme
 
 ## Citation
 
-If you use this model, please cite SAM2 and the AtlasPatch project. A formal paper is forthcoming.
+If you use this model, please cite our paper:
+
+```bibtex
+@article{atlaspatch2025,
+  title   = {AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing in Computational Pathology},
+  author  = {Alagha, Ahmed and Leclerc, Christopher and Kotp, Yousef and Abdelwahed, Omar and Moras, Calvin and Rentopoulos, Peter and Rostami, Rose and Nguyen, Bich Ngoc and Baig, Jumanah and Khellaf, Abdelhakim and Trinh, Vincent Quoc-Huy and Mizouni, Rabeb and Otrok, Hadi and Bentahar, Jamal and Hosseini, Mahdi S.},
+  journal = {arXiv},
+  year    = {2025},
+  url     = {TODO: coming soon}
+}
+```