MERFISH - Mouse Cortex

Spatially resolved profiling of mouse cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).

reference Fang et al., 2022

Mus musculus Organism

13,221 × 234 Dimensions

12.54 MiB Size

log_cp10k Normalization

26-09-2024 Created

Source

Description

Spatially resolved profiling of mouse cerebral cortex (visual cortex (VIS), auditory cortex (AUD) and temporal association area (TEa) unexpanded sections) using multiplexed error-robust fluorescence in situ hybridization (MERFISH).

Preview

An AnnData object with n_obs × n_vars = 13,221 × 234 with slots:

var: feature_name

layers: counts

uns: dataset_description , dataset_id , dataset_name , dataset_organism , dataset_reference , dataset_summary , dataset_url

Data structure

Name	Description	Type	Data type	Size
var
`feature_name`	A human-readable name for the feature, usually a gene symbol.	vector	object	234
layers
`counts`	Raw counts	densematrix	float32	13221 × 234
uns
`dataset_description`	Long description of the dataset.	atomic	str	1
`dataset_id`	A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived.	atomic	str	1
`dataset_name`	A human-readable name for the dataset.	atomic	str	1
`dataset_organism`	The organism of the sample in the dataset.	atomic	str	1
`dataset_reference`	Bibtex reference of the paper in which the dataset was published.	atomic	str	1
`dataset_summary`	Short description of the dataset.	atomic	str	1
`dataset_url`	Link to the original source of the dataset.	atomic	str	1

Download & explore

The processed dataset lives on the OpenProblems public S3 bucket, which is world-readable. Download the file directly, or copy its S3 URI to fetch it with your tool of choice.

dataset.h5ad 12.54 MiB

Download

s3://openproblems-data/resources/datasets/zenodo_spatial/merfish/mouse_cortex/dataset.h5ad

Used in

Spatially Variable Genes

References

Fang, R., Xia, C., Close, J. L., Zhang, M., He, J., Huang, Z., Halpern, A. R., Long, B., Miller, J. A., Lein, E. S., & Zhuang, X. (2022). Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. 10.1126/science.abm1741 ↗