MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-1)#

4.2 million cell spatial transcriptomics dataset spanning 147 coronal sections with a 1122 gene panel and mapped to the whole mouse brain taxonomy and Allen-CCF-2020. We performed MERFISH imaging on 150 coronal sections from this animal, obtained 4.8 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 three fractured tissue slices and 4.7 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 18 slices that are at the anterior and posterior ends of the brain and cannot be registered to the CCF, we manually aligned and oriented these 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, therefore multiple anterior slices have a “0” value for their z coordinates. 4.2 million cells remained after this step. The cell-by-gene matrix of the 4.2 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. 3.4 million cells passed the confidence score threshold for cell subclass label transfer and 2.8 million cells further passed the confidence score threshold for cell cluster label transfer. These 2.8 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 2.6 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 for more details.

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


Current Version


Expression Matrices


3.09 GB



1.33 GB

CCF Coordinates


0.21 GB

Data is being share under the CC BY 4.0 license.

Associated notebooks: