AOI, area of illumination; BICCN, Brain Initiative Cell Census Network; BOLORAMIS, barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses; Baysor, Bayesian Segmentation of Spatial Transcriptomics Data; BinSpect, Binary Spatial Extraction; CCC, cell­cell communication; CCI, cell­cell interactions; CNV, copy-number variation; Computational biology; DSP, digital spatial profiling; DbiT-Seq, Deterministic Barcoding in Tissue for spatial omics sequencing; FA, factor analysis; FFPE, formalin-fixed, paraffin-embedded; FISH, fluorescence in situ hybridization; FISSEQ, fluorescence in situ sequencing of RNA; FOV, Field of view; GRNs, gene regulation networks; GSEA, gene set enrichment analysis; GSVA, gene set variation analysis; HDST, high definition spatial transcriptomics; HMRF, hidden Markov random field; ICG, interaction changed genes; ISH, in situ hybridization; ISS, in situ sequencing; JSTA, Joint cell segmentation and cell type annotation; KNN, k-nearest neighbor; LCM, Laser Capture Microdissection; LCM-seq, laser capture microdissection coupled with RNA sequencing; LOH, loss of heterozygosity analysis; MC, Molecular Cartography; MERFISH, multiplexed error-robust FISH; NMF (NNMF), Non-negative matrix factorization; PCA, Principal Component Analysis; PIXEL-seq, Polony (or DNA cluster)-indexed library-sequencing; PL-lig, padlock ligation; QC, quality control; RNAseq, RNA sequencing; ROI, region of interest; SCENIC, Single-Cell rEgulatory Network Inference and Clustering; SME, Spatial Morphological gene Expression normalization; SPATA, SPAtial Transcriptomic Analysis; ST Pipeline, Spatial Transcriptomics Pipeline; ST, Spatial transcriptomics; STARmap, spatially-resolved transcript amplicon readout mapping; Single-cell analysis; Spatial data analysis frameworks; Spatial deconvolution; Spatial transcriptomics; TIVA, Transcriptome in Vivo Analysis; TMA, tissue microarray; TME, tumor micro environment; UMAP, Uniform Manifold Approximation and Projection for Dimension Reduction; UMI, unique molecular identifier; ZipSeq, zipcoded sequencing.; scRNA-seq, single-cell RNA sequencing; scvi-tools, single-cell variational inference tools; seqFISH, sequential fluorescence in situ hybridization; sequ-smFISH, sequential single-molecule fluorescent in situ hybridization; smFISH, single molecule FISH; t-SNE, t-distributed stochastic neighbor embedding