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

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

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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.
• 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
2	Dataset2_MolecularCartography_cardiomyocytes	Molecular Cartography	Human / Heart	4	figshare
3	Dataset3_STARmap_MouseBrain	STARmap	Mouse / Brain	12	Google Drive
4	Dataset4_merscope_MouseLiver	MERFISH	Mouse / Liver	1	Vizgen
5	Dataset5_merfish_u2os	MERFISH	Human / Bone	1	figshare
6	Dataset6_merfish_intestine	MERFISH	Mouse / Intestine	1	Dryad
7	Dataset7_merfish_MurineGut	MERFISH	Mouse / Gut	8	Dryad
8	Dataset8_merfish_HumanLiverDonors	MERFISH	Human / Liver	2	Zenodo
9	Dataset9_Xenium_HumanOvarianCancer	Xenium	Human / Ovary	1	SPATCH (PKU Genomics)
10	Dataset10_Xenium_MouseBrain	Xenium	Mouse / Brain	6	10x Genomics
11	Dataset11_Xenium_HumanBrain	Xenium	Human / Brain	3	10x Genomics
12	Dataset12_Xenium_HumanColon	Xenium	Human / Colon	4	10x Genomics
13	Dataset13_Xenium_HumanLungCancer	Xenium	Human / Lung	2	10x Genomics
14	Dataset14_Xenium_HumanPancreas	Xenium	Human / Pancreas	1	10x Genomics
15	Dataset15_Xenium_HumanOvarianCancer	Xenium	Human / Ovary	1	10x Genomics
16	Dataset16_Xenium_HumanBreastCancer	Xenium	Human / Breast	3	10x Genomics
17	Dataset17_Xenium_HumanLymphomaCancer	Xenium	Human / Lymphoid	3	Zenodo
18	Dataset18_Xenium_HumanBladderCancer	Xenium	Human / Bladder	1	Zenodo
19	Dataset19_Xenium_HumanColorectalCancer	Xenium	Human / Colorectum	3	Zenodo
20	Dataset20_Xenium_HumanLungCancer	Xenium	Human / Lung	3	Zenodo
21	Dataset21_Xenium_HumanBreastCancer	Xenium	Human / Breast	3	Zenodo
22	Dataset22_Xenium_HumanOvarianCancer	Xenium	Human / Ovary	3	Zenodo
23	Dataset23_CosMx_HumanLungAdenocarcinoma	CosMx	Human / Lung	1	GEO GSM9046088 (series GSE299786)
24	Dataset24_CosMx_HumanMesothelioma	CosMx	Human / Pleural	1	GEO GSM9046090 (series GSE299786)
25	Dataset25_CosMx_HEK293T	CosMx	Human / Kidney	1	pending
26	Dataset26_CosMx_HumanOvarianCancer	CosMx	Human / Ovary	1	SPATCH (PKU Genomics)
27	Dataset27_CosMx_HumanLiverCancer	CosMx	Human / Liver	1	SPATCH (PKU Genomics)
28	Dataset28_CosMx_HumanBreastCancer	CosMx	Human / Breast	1	Zenodo
29	Dataset29_CosMx_HumanLungCancer	CosMx	Human / Lung	1	Zenodo
30	Dataset30_CosMx_HumanOvarianCancer	CosMx	Human / Ovary	1	Zenodo
31	Dataset31_CosMx_HumanColorectalCancer	CosMx	Human / Colorectum	1	Zenodo
32	Dataset32_CosMx_HumanLymphomaCancer	CosMx	Human / Lymphoid	1	pending
33	Dataset33_merfish_u2os	MERFISH	Human / Bone	7	Zhuang Lab
34	Dataset34_Xenium_MouseBrain	Xenium	Mouse / Brain	3	10x Genomics
35	Dataset35_CosMx_HumanLung	CosMx	Human / Lung	8	Bruker / NanoString

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