Table 1.

Important technologies reviewed

Field	Technique	Description	Published plants study?
Transcriptomics	scRNA-seq	Extracting transcriptomic data from individual cells	Jean-Baptiste et al. (2019); Nelms and Walbot (2019); Ryu et al. (2019); Shulse et al. (2019); Satterlee et al. (2020); Shaw et al. (2021); Liu et al. (2021); Xu et al. (2021)
	ST	First array-based ST platform; 100-µm spot capture resolution	Giacomello et al. (2017); Giacomello and Lundeberg (2018)
	Visium spatial gene expression (10× Genomics)	Upgraded resolution from ST; 55-µm spot capture resolution	No
	HDST	Uses microbeads and a sequential hybridization strategy for high resolution spatial capture; microbeads are 2 µm	No
	Slide-seq; Slide-seq V2	Employs slides covered with pucks of 10-µm microbeads coated with poly-T capture probes	No
	XYZeq	Combines scRNA-seq and ST by using two rounds of split-pool indexing to capture the spatial information of each cell at a relatively low resolution (500 µm) followed by making indexed scRNA-seq libraries	No
	ExSeq	Combines ExM and in situ sequencing and hybridization to enable large-scale, spatially resolved transcript identification and localization	No
3D imaging	XRM	A specialized XCT system that incorporates microscope objective lenses in the beam path, allowing for high resolution, multiscale 3D imaging over a wide range of sample sizes	Duncan et al. (2021)
	ExM	A technique that anchors cell molecules to a nearby scaffold and expands many-fold while maintaining relative molecular relationships	Kao and Nodine (2019, 2021)
	LSFM	A nondestructive technique that uses a thin plane of light to section and view tissues as low as subcellular resolution	Berthet and Maizel (2016); Ovečka et al. (2018, 2021)
	XCT	Generates 2D radiographs by passing X-rays through a sample onto a detector, and computationally reconstructing the images into a 3D volume	Aylmore (1993); Heeraman et al. (1997); Stuppy et al. (2003); Kaminuma et al. (2008); Leroux et al. (2009); Dhondt et al. (2010); and van der Niet et al. (2010)