# MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-2)

1.9 million cell spatial transcriptomics dataset spanning 66 coronal 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 67 coronal sections from
this animal, obtained 2.1 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 one fractured tissue slice and 2.0 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 midline
and removed cells that substantially passed the midline in the other hemisphere
(which has not been registered to the CCF). For the 13 slices that are at the
anterior and posterior ends of the brain and cannot be registered to the CCF,
we manually aligned and oriented the slices to determine the coordinates of the
center point of the midline.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 anterior-posterior axis based on either the registration
results (for slices that can be registered to CCF) or anterior-posterior
positions of the slices measured during tissue sectioning (for the slices that
cannot be registered). The z position is set to zero when the estimated
position becomes zero or negative. 1.9 million cells remained after this step.
The cell-by-gene matrix of the 1.9 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. 1.5 million cells passed the confidence score threshold for cell
subclass label transfer and 1.2 million cells further passed the confidence
score threshold for cell cluster label transfer. These 1.2 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 1.1 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-2/20230830/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/Zhuang-ABCA-2/20230830/) | 1.30 GB |
| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-2/20241115](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-2/20241115/) | 0.57 GB |
| CCF Coordinates | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-2-CCF/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-2-CCF/20230830/) | 0.08 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 AbcProjectcache 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