Figure 1 | Scientific Reports

Figure 1

From: Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

Figure 1

Overview of the SpaceTx analysis workflow. The reference scRNA-seq cell types of the primary visual cortex (VISp) of mouse brain are from Tasic et al.4. Spatial transcriptomics data were generated by four image-based experimental protocols (MERFISH, smFISH, BaristaSeq, and ExSeq). Segmentation and quality control were performed using a common procedure (Baysor). Six computational algorithms (ATLAS, FR-Match, map.cells*, mfishtools, pciSeq, and Tangram) for cell type matching were applied. Two meta-analysis strategies were used to combine the individual matching results. Spot-based segmentation-free cell type assignment was conducted using SSAM. All data and matching results can be viewed in Cytosplore Viewer (https://viewer.cytosplore.org).

Back to article page