MERFISH
Datasets
All datasets matching “MERFISH”merfish
MERFISH Mouse Brain Dataset
This dataset provides spatial transcriptomic profiles of the adult mouse brain using MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enabling high-resolution cellular gene expression analysis in situ. The MERFISH data consists of 59 coronal sections (10 micron thick) covering the whole anterior to posterior extent of the brain (~200 micron apart) from a single adult male mouse.
It includes both raw and processed versions of the data… See the full description on the dataset page: https://huggingface.co/datasets/cgeorgiaw/merfish.mah2024_merfishst-recon-merfish-breast-cancer
MERFISH Breast Cancer 3D Cell Reconstruction Dataset
Processed MERFISH spatial transcriptomics data (HumanBreastCancerPatient1) for 3D cell shape reconstruction.
Structure
trainval.h5 — 196GB train/val split with cell point clouds and features
trainval_annotations.h5 — 4.9MB train/val cell type annotations
trainval_indices.npy — 857KB train/val cell indices
test.h5 — 22GB test split with cell point clouds and features
test_annotations.h5 — 553KB test cell type… See the full description on the dataset page: https://huggingface.co/datasets/kanand123/st-recon-merfish-breast-cancer.mousehypothalamus_merfish_moffitt # Mouse Hypothalamic Preoptic Region MERFISH · Moffitt 2018
Curated, ready-to-load spatial transcriptomics dataset.
## Source
- Paper: [Moffitt et al., Science 2018](https://www.science.org/doi/10.1126/science.aau5324)
- Canonical download: Bioconductor MerfishData::MouseHypothalamusMoffitt2018() — mirrors Dryad doi:10.5061/dryad.8t8s248
## Scale
| Property | Value |
|---|---|
| Technology | MERFISH (135 smFISH + 21 seqFISH = 156 genes) |
| Species… See the full description on the dataset page: https://huggingface.co/datasets/Shaow/mousehypothalamus_merfish_moffitt.mousebrain_merfish_zhuang # Whole Mouse Brain MERFISH · Zhuang ABCA-4
Curated, ready-to-load spatial transcriptomics dataset.
## Source
- Paper: [Zhang, Jung, Zhuang et al., Nature 2023](https://www.nature.com/articles/s41586-023-06808-9)
- Canonical download: Brain Image Library doi 10.35077/act-bag · counts_mouse4_sagittal subset
## Scale
| Property | Value |
|---|---|
| Technology | MERFISH (1147-gene panel) |
| Species | Mus musculus |
| Tissue | Whole mouse brain… See the full description on the dataset page: https://huggingface.co/datasets/Shaow/mousebrain_merfish_zhuang.Merfishreportpipeline