| --- |
| license: cc-by-4.0 |
| pretty_name: STRAND |
| tags: |
| - biology |
| - spatial-transcriptomics |
| - single-cell |
| - subcellular |
| --- |
| |
| # STRAND — Subcellular Transcript RNA Architecture and Navigation Database |
|
|
| STRAND is a curated collection of **subcellular-resolution spatial transcriptomics** datasets, |
| harmonized into a single processed format for downstream analysis (cell-type annotation, |
| RNA localization patterns, colocalization, compartment/RNAflux, segmentation QC). |
|
|
| ## Overview |
|
|
| - **35 datasets / 95 samples** (~236 GB total) |
| - **Platforms:** MERFISH, SeqFISH+, Molecular Cartography, STARmap, Xenium, CosMx, MERSCOPE |
| - **Species:** human, mouse |
| - **Tissues:** brain, liver, gut/intestine, pancreas, and multiple cancer types |
| (ovarian, breast, lung, colorectal, bladder, lymphoma, mesothelioma, ...) |
|
|
| ## File Organization |
|
|
| Each dataset has its own folder. Datasets with multiple samples/slices contain multiple `.pkl` files: |
|
|
| ``` |
| Dataset10_Xenium_MouseBrain/ |
| ├── Dataset10_1_Xenium_MouseBrain_data_dict.pkl |
| ├── Dataset10_2_Xenium_MouseBrain_data_dict.pkl |
| └── ... |
| Dataset26_CosMx_HumanOvarianCancer/ |
| └── Dataset26_CosMx_HumanOvarianCancer_data_dict.pkl |
| ``` |
|
|
| The folder name encodes `Dataset<N>_<platform>_<tissue>`; the file name additionally carries |
| the sample/slice index. |
|
|
| ## Data Format |
|
|
| Each `*_data_dict.pkl` is a Python `dict` (standard `pickle`) with the following keys: |
|
|
| | Key | Type | Description | |
| |---|---|---| |
| | `data_df` | `DataFrame` | Transcript-level table, one row per detected transcript. Columns: `cell, gene, x, y, z, umi` (`x/y/z` in microns, `umi` = count). | |
| | `coordinates` | `DataFrame` | Per-cell table: cell centers plus `fov` and `batch` columns (each cell's field-of-view / batch membership). | |
| | `expression` | `DataFrame` | Cell × gene expression matrix (wide format). | |
| | `cell_boundary` | `dict` | `{cell_id: DataFrame(x, y)}` — polygon vertices of each cell's segmentation boundary. | |
| | `nuclear_boundary` | `dict` | `{cell_id: DataFrame(x, y)}` — polygon vertices of each nucleus (only for datasets with nuclear segmentation / DAPI). | |
| | `metadata` | `dict` | Dataset-level metadata (platform, tissue, species, etc.). | |
|
|
| **Notes** |
| - `data_df` has **no** `fov` column — a transcript's FOV is resolved by joining its `cell` to |
| `coordinates` (cell → fov). |
| - **CosMx** datasets additionally contain an `unassigned_data_df` (free transcripts with `cell = NA`). |
| - Column dtypes may vary across platforms (e.g. CosMx uses `category`/`float32`/`int16`); read tolerantly. |
|
|
| ## Loading |
|
|
| ```python |
| import pickle |
| |
| path = "Dataset26_CosMx_HumanOvarianCancer/Dataset26_CosMx_HumanOvarianCancer_data_dict.pkl" |
| with open(path, "rb") as f: |
| d = pickle.load(f) |
| |
| print(d.keys()) |
| print(d["data_df"].head()) # transcripts: cell, gene, x, y, z, umi |
| print(d["coordinates"].columns) # cell centers + fov, batch |
| ``` |
|
|
| --- |
|
|
| ## 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 | [GEO GSM9046088](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM9046088) (series [GSE299786](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299786)) | |
| | 24 | `Dataset24_CosMx_HumanMesothelioma` | CosMx | Human / Pleural | 1 | [GEO GSM9046090](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM9046090) (series [GSE299786](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299786)) | |
| | 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 |
|
|
|
|
