# About cell type for middle temporal gyrus reference dataset

**URL:** <https://community.brain-map.org/t/about-cell-type-for-middle-temporal-gyrus-reference-dataset/3853>\
**Category:** Technical\
**Created:** [November 14, 2024, 7:48pm UTC](https://community.brain-map.org/t/about-cell-type-for-middle-temporal-gyrus-reference-dataset/3853 "2024-11-14T19:48:01Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Chris\_D](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/chris_d/32/1823_2.png) [@Chris\_D](https://community.brain-map.org/u/Chris_D)\
**Post date:** [November 14, 2024, 7:48pm UTC](https://community.brain-map.org/t/about-cell-type-for-middle-temporal-gyrus-reference-dataset/3853/1 "2024-11-14T19:48:01Z")

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Hi all,

I try to do cell type annotation for a visium data from middle temporal gyrus, so I follow seurat tutorial here:

> **[Analysis, visualization, and integration of Visium HD spatial datasets with...](https://satijalab.org/seurat/articles/spatial_vignette)**
>
> Seurat

The reference has these cell types in subclass\_label column: “Pax6”, “L5/6 NP”, “L5 IT”, “L6 CT”, “L4 IT”, “Astrocyte”, “L2/3 IT”, “Vip”, “Sst Chodl”, “L6 IT Car3”, “L6 IT”, “Sncg”, “Pvalb”, “Oligodendrocyte”, “Lamp5 Lhx6”, “Sst”, “VLMC”, “Lamp5”, “Microglia-PVM”, “OPC”, “L6b”, “Endothelial”, “L5 ET”, “Chandelier”, “max”  
However, when using SpatialFeaturePlot(), I got no signal of cell types that should have such as microglia

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/1/175e2937fda7fd2f502b9f90cf72ed86c9d5a1a7.jpeg)

I use the data from this paper: [Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease | Acta Neuropathologica Communications | Full Text](https://actaneurocomms.biomedcentral.com/articles/10.1186/s40478-022-01494-6)  
Would you please have a suggestion?