---
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