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README.md

@@ -1,3 +1,55 @@
----
-license: mit
----
+---
+license: mit
+tags:
+  - cryo-et
+  - tomography
+  - segmentation
+  - biology
+  - microscopy
+  - sam
+  - medsam
+pretty_name: AgentProject XuLab — CryoET Large Files
+size_categories:
+  - 1B<n<10B
+---
+
+# AgentProject XuLab — Large Files
+
+This dataset hosts large binary files for the [AgentProject_XuLab](https://github.com/vatsal-ts/AgentProject_XuLab) repository, which is part of the XuLab research project on AI-driven Cryo-Electron Tomography (CryoET) analysis.
+
+These files are stored here due to GitHub's 100MB file size limit.
+
+## Contents
+
+| File | Size | Description |
+|---|---|---|
+| `sam_vit_b_01ec64.pth` | 358 MB | SAM (Segment Anything Model) ViT-B checkpoint |
+| `medsam_vit_b.pth` | 358 MB | MedSAM ViT-B checkpoint (medical image segmentation) |
+| `tomograms/local.mrc` | 1.6 GB | CryoET tomogram — full volume (NPC1-deficient HEK293T cells) |
+| `tomograms/mitochondrion_20036.mrc` | 385 MB | CryoET tomogram — mitochondrion annotation volume |
+
+## About the Data
+
+The tomogram files are from a CryoET dataset of **NPC1-deficient human HEK293T cells** with annotations for multiple cellular features including lysosomes, mitochondria, and membranes.
+
+The `.pth` files are pretrained model weights used by the CryoETAgent pipeline for organelle segmentation:
+- **SAM** ([Kirillov et al., 2023](https://arxiv.org/abs/2304.02643)) — general-purpose segmentation
+- **MedSAM** ([Ma et al., 2024](https://www.nature.com/articles/s41467-024-44824-z)) — SAM fine-tuned for medical/biological imaging
+
+## Usage
+
+Clone the GitHub repo and run the download script:
+
+```bash
+git clone https://github.com/vatsal-ts/AgentProject_XuLab
+cd AgentProject_XuLab
+pip install huggingface_hub
+python download_large_files.py
+```
+
+This will place all files in their correct locations automatically.
+
+## Related
+
+- GitHub repo: [vatsal-ts/AgentProject_XuLab](https://github.com/vatsal-ts/AgentProject_XuLab)
+- CryoETAgent: AI agent for automated CryoET organelle analysis