Add CC BY 4.0 license and per-dataset source attribution

README.md

@@ -1,4 +1,5 @@
 ---
+license: cc-by-4.0
 pretty_name: STRAND
 tags:
 - biology
@@ -72,4 +73,61 @@ print(d["coordinates"].columns)  # cell centers + fov, batch
 
 ---
 
-*Source attribution and citation information will be added upon publication.*
+## License and attribution
+
+The curated files in this repository are **derived** works: each dataset was re-processed from a
+publicly available, previously published dataset into the unified STRAND format described above.
+
+- **This curated collection** (harmonized `.pkl` files, folder structure and metadata) is released
+  under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).
+- **The underlying data** remain subject to the terms of their original sources, listed per dataset
+  below. Users who redistribute or publish analyses based on these files should cite both STRAND and
+  the original study/repository of the dataset(s) used.
+
+## Source datasets
+
+| # | Folder | Platform | Species / tissue | Samples | Original source |
+|---|---|---|---|---|---|
+| 1 | `Dataset1_seqfish+_fibroblast` | SeqFISH+ | Mouse / Skin | 1 | [figshare](https://figshare.com/collections/Bento_Manuscript_Datasets/6564043/1) |
+| 2 | `Dataset2_MolecularCartography_cardiomyocytes` | Molecular Cartography | Human / Heart | 4 | [figshare](https://figshare.com/collections/Bento_Manuscript_Datasets/6564043/1) |
+| 3 | `Dataset3_STARmap_MouseBrain` | STARmap | Mouse / Brain | 12 | [Google Drive](https://drive.google.com/drive/folders/1cmLLO9elJYb8VOH0XK6yHK8d3ehMDzfq?usp=sharing) |
+| 4 | `Dataset4_merscope_MouseLiver` | MERFISH | Mouse / Liver | 1 | [Vizgen](https://info.vizgen.com/mouse-liver-data?submissionGuid=832a9f61-22d3-44c1-a2cf-838c166d9ac5) |
+| 5 | `Dataset5_merfish_u2os` | MERFISH | Human / Bone | 1 | [figshare](https://figshare.com/collections/Bento_Manuscript_Datasets/6564043/1) |
+| 6 | `Dataset6_merfish_intestine` | MERFISH | Mouse / Intestine | 1 | [Dryad](https://doi.org/10.5061/dryad.jm63xsjb2) |
+| 7 | `Dataset7_merfish_MurineGut` | MERFISH | Mouse / Gut | 8 | [Dryad](https://datadryad.org/dataset/doi:10.5061/dryad.p5hqbzm0z) |
+| 8 | `Dataset8_merfish_HumanLiverDonors` | MERFISH | Human / Liver | 2 | [Zenodo](https://zenodo.org/records/17735506) |
+| 9 | `Dataset9_Xenium_HumanOvarianCancer` | Xenium | Human / Ovary | 1 | [SPATCH (PKU Genomics)](https://spatch.pku-genomics.org/#/download) |
+| 10 | `Dataset10_Xenium_MouseBrain` | Xenium | Mouse / Brain | 6 | [10x Genomics](https://www.10xgenomics.com/datasets/xenium-in-situ-analysis-of-alzheimers-disease-mouse-model-brain-coronal-sections-from-one-hemisphere-over-a-time-course-1-standard) |
+| 11 | `Dataset11_Xenium_HumanBrain` | Xenium | Human / Brain | 3 | [10x Genomics](https://www.10xgenomics.com/datasets/xenium-human-brain-preview-data-1-standard) |
+| 12 | `Dataset12_Xenium_HumanColon` | Xenium | Human / Colon | 4 | [10x Genomics](https://www.10xgenomics.com/datasets/human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard) |
+| 13 | `Dataset13_Xenium_HumanLungCancer` | Xenium | Human / Lung | 2 | [10x Genomics](https://www.10xgenomics.com/datasets/xenium-human-lung-cancer-post-xenium-technote) |
+| 14 | `Dataset14_Xenium_HumanPancreas` | Xenium | Human / Pancreas | 1 | [10x Genomics](https://www.10xgenomics.com/datasets/ffpe-human-pancreas-with-xenium-multimodal-cell-segmentation-1-standard) |
+| 15 | `Dataset15_Xenium_HumanOvarianCancer` | Xenium | Human / Ovary | 1 | [10x Genomics](https://www.10xgenomics.com/datasets/xenium-prime-ffpe-human-ovarian-cancer) |
+| 16 | `Dataset16_Xenium_HumanBreastCancer` | Xenium | Human / Breast | 3 | [10x Genomics](https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast) |
+| 17 | `Dataset17_Xenium_HumanLymphomaCancer` | Xenium | Human / Lymphoid | 3 | [Zenodo](https://doi.org/10.5281/zenodo.18000256) |
+| 18 | `Dataset18_Xenium_HumanBladderCancer` | Xenium | Human / Bladder | 1 | [Zenodo](https://doi.org/10.5281/zenodo.17986017) |
+| 19 | `Dataset19_Xenium_HumanColorectalCancer` | Xenium | Human / Colorectum | 3 | [Zenodo](https://doi.org/10.5281/zenodo.18000256) |
+| 20 | `Dataset20_Xenium_HumanLungCancer` | Xenium | Human / Lung | 3 | [Zenodo](https://doi.org/10.5281/zenodo.18000256) |
+| 21 | `Dataset21_Xenium_HumanBreastCancer` | Xenium | Human / Breast | 3 | [Zenodo](https://doi.org/10.5281/zenodo.18000256) |
+| 22 | `Dataset22_Xenium_HumanOvarianCancer` | Xenium | Human / Ovary | 3 | [Zenodo](https://doi.org/10.5281/zenodo.18000256) |
+| 23 | `Dataset23_CosMx_HumanLungAdenocarcinoma` | CosMx | Human / Lung | 1 | [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) |
+| 24 | `Dataset24_CosMx_HumanMesothelioma` | CosMx | Human / Pleural | 1 | [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) |
+| 25 | `Dataset25_CosMx_HEK293T` | CosMx | Human / Kidney | 1 | *pending* |
+| 26 | `Dataset26_CosMx_HumanOvarianCancer` | CosMx | Human / Ovary | 1 | [SPATCH (PKU Genomics)](https://spatch.pku-genomics.org/#/download) |
+| 27 | `Dataset27_CosMx_HumanLiverCancer` | CosMx | Human / Liver | 1 | [SPATCH (PKU Genomics)](https://spatch.pku-genomics.org/#/download) |
+| 28 | `Dataset28_CosMx_HumanBreastCancer` | CosMx | Human / Breast | 1 | [Zenodo](https://doi.org/10.5281/zenodo.17986017) |
+| 29 | `Dataset29_CosMx_HumanLungCancer` | CosMx | Human / Lung | 1 | [Zenodo](https://doi.org/10.5281/zenodo.17986017) |
+| 30 | `Dataset30_CosMx_HumanOvarianCancer` | CosMx | Human / Ovary | 1 | [Zenodo](https://doi.org/10.5281/zenodo.17986017) |
+| 31 | `Dataset31_CosMx_HumanColorectalCancer` | CosMx | Human / Colorectum | 1 | [Zenodo](https://doi.org/10.5281/zenodo.17986017) |
+| 32 | `Dataset32_CosMx_HumanLymphomaCancer` | CosMx | Human / Lymphoid | 1 | *pending* |
+| 33 | `Dataset33_merfish_u2os` | MERFISH | Human / Bone | 7 | [Zhuang Lab](http://zhuang.harvard.edu/MERFISHData/data_for_release.zip) |
+| 34 | `Dataset34_Xenium_MouseBrain` | Xenium | Mouse / Brain | 3 | [10x Genomics](https://www.10xgenomics.com/datasets/fresh-frozen-mouse-brain-replicates-1-standard) |
+| 35 | `Dataset35_CosMx_HumanLung` | CosMx | Human / Lung | 8 | [Bruker / NanoString](https://brukerspatialbiology.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/nsclc-ffpe-dataset/) |
+
+*Two entries are still pending source confirmation and will be completed in a future revision.*
+
+## Citation
+
+STRAND: A Comprehensive Subcellular-Resolved Spatial Transcriptome RNA Architecture and Navigation
+Database. Manuscript in preparation. Database: https://strand.phasep.pro
+