| # STimage-1K4M Dataset | |
| Welcome to the STimage-1K4M Dataset repository. This dataset is designed to foster research in the field of spatial transcriptomics, combining high-resolution histopathology images with detailed gene expression data. | |
|  | |
| ## Dataset Description | |
| STimage-1K4M consists of 1,149 spatial transcriptomics slides, totaling over 4 million spots with paired gene expression data. This dataset includes: | |
| - Images. | |
| - Gene expression profiles matched with high-resolution histopathology images. | |
| - Spatial coordinates for each spot. | |
| ## Data structure | |
| The data structure is organized as follows: | |
| ```bash | |
| ├── annotation # Pathologist annotation | |
| ├── meta # Test files (alternatively `spec` or `tests`) | |
| │ ├── bib.txt # the bibtex for all studies with pmid included in the dataset | |
| │ ├── meta_all_gene.csv # The meta information | |
| ├── ST # Include all data for tech: Spatial Transcriptomics | |
| │ ├── coord # Include the spot coordinates & spot radius of each slide | |
| │ ├── gene_exp # Include the gene expression of each slide | |
| │ └── image # Include the image each slide | |
| ├── Visium # Include all data for tech: Visium, same structure as ST | |
| ├── VisiumHD # Include all data for tech: VisiumHD, same structure as ST | |
| ``` | |
| ## Repository structure | |
| The code for data processing and reproducing evaluation result in the paper are in [Document](https://jiawenchenn.github.io/STimage-1K4M/docs/01-make-meta). | |
| ## Acknowledgement | |
| The fine-tuning and evaluation codes borrows heavily from [CLIP](https://github.com/openai/CLIP/issues/83) and [PLIP](https://github.com/PathologyFoundation/plip/). | |
| ## Citation | |
| ``` | |
| @misc{chen2024stimage1k4m, | |
| title={STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics}, | |
| author={Jiawen Chen and Muqing Zhou and Wenrong Wu and Jinwei Zhang and Yun Li and Didong Li}, | |
| year={2024}, | |
| eprint={2406.06393}, | |
| archivePrefix={arXiv}, | |
| primaryClass={cs.CV} | |
| } | |
| ``` | |
| ## License | |
| All code is licensed under the MIT License - see the LICENSE.md file for details. |