# MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-3)

2.1 million cell spatial transcriptomics dataset spanning 23 sagittal sections
with a 1122 gene panel and mapped to the  [whole mouse brain taxonomy](WMB-taxonomy.md) and
[Allen-CCF-2020](Allen-CCF-2020.md). We performed MERFISH imaging on 25 sagittal sections
from this animal, obtained 2.2 million segmented cells that passed quality
control, and integrated the MERFISH data (including data from all four animals)
with the scRNA-seq data from the Allen Institute to classify cells. We applied
a series of filters to select a subset of cells to be visualized on the ABC
atlas. We first removed two fractured tissue slice and 2.1 million cells
remained after this step. Then we aligned the spatial coordinates of the cells
to the Allen-CCF-2020. For the slices that can be registered to the CCF, we
used the CCF coordinates to define the coordinates of the center point of the
tissue and removed cells that substantially passed the posterior edge (which
has not been registered to the CCF). For the 3 lateral slices that cannot be
registered to the CCF, we manually aligned and oriented the slices. The x, y
coordinates are experimentally measured coordinates after rotating and aligning
the tissue slices to the CCF, and the z coordinates are estimated position of
each tissue slice in the 3D Allen-CCF 2020 space along the medial-lateral axis
based on either the registration results (for slices that can be registered to
CCF) or medial-lateral positions of the slices measured during tissue
sectioning (for the slices that cannot be registered). 2.1 million cells
remained after this step. The cell-by-gene matrix of the 2.1 millions cells can
be downloaded from the AWS bucket of this animal. We then filtered the cells by
cell-classification (label transfer) confidence scores calculated during
MERFISH-scRNAseq data integration. 1.8 million cells passed the confidence
score threshold for cell subclass label transfer and 1.6 million cells further
passed the confidence score threshold for cell cluster label transfer. These
1.6 million cells are included in the cell metadata file that can be downloaded
from the AWS bucket and are displayed on the ABC Atlas. The CCF coordinates of
the 1.6 million cells that were registered to the 3D Allen-CCF can be
downloaded from the CCF coordinate file in the AWB bucket. Refer to
[Zhang et al. 2023](https://doi.org/10.1101/2023.03.06.531348) for more details.

The expression matrices and associated metadata is hosted on AWS S3 bucket as a
AWS Public Dataset:

| Component | Current Version | Size |
|---|--|---|
| Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/Zhuang-ABCA-3/20230830/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/Zhuang-ABCA-3/20230830/) | 1.69 GB |
| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-3/20241115](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-3/20241115/) | 0.75 GB |
| CCF Coordinates | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-3-CCF/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-3-CCF/20230830/) | 0.12 GB |

Data is being share under the CC BY 4.0 license.

Associated notebooks:
* [**Getting started**](../notebooks/getting_started.ipynb): learn how to use the manifest.json file to
  facilitate data download and usage.
* [**MERFISH whole mouse brain spatial transcriptomics**](../notebooks/zhuang_merfish_tutorial.ipynb): learn about the
  MERFISH dataset through some example use cases and visualization