| --- |
| 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 |
|
|
