Journal: bioRxiv

Article Title: Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics

doi: 10.1101/2023.03.31.535025

Figure Lengend Snippet: a , Data processing and filtering. Accepted SRT data types for analysis, processing and filtering using the AW include Visium, MERFISH and Xenium. Analysis steps available to all SRT data types and menu with examples of available visualisations after data analysis. On the right, an example of heatmap of read counts generated for invasive ductal carcinoma breast tissue data generated with Visium from 10X Genomics . b , Leiden clustering analysis and visualisation of clustering output using Visium data of the human cerebral cortex . c, Identification of SVGs is performed using SpatialDE for Visium data and by calculating Moran’s I statistic for MERFISH and Xenium. d , Examples of output files generated by AW workflow with example data from coronal mouse kidney section generated by Visium . e, The user interface allows for alignment of multiple, serial Visium slides (e i ) uploaded in tandem (e ii ) so they can be combined into a 3D object ( e iii ), demonstrated here with data from the human embryonic heart at 6 dpc .The tissue images are used for reference.

Article Snippet: We envision expanding the AW to include pre-processing pipelines for data from SRT platforms beyond Visium, Xenium and MERFISH (e.g ., Stereopy package for STOmics and a cell segmentation pipeline for image based technologies).

Techniques: Generated

Journal: bioRxiv

Article Title: Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics

doi: 10.1101/2023.03.31.535025

Figure Lengend Snippet: a, Gene search. a i , Gene search bar options for visualisation of selected gene expression patterns across a tissue. a ii , A scale of gene expression can be visualised with a colour map indicating the relative expression levels of the selected gene at each location. The colour map uses a blue to red gradient, with lower expression levels corresponding to colours on the blue end of the spectrum and higher expression levels corresponding to colours on the red side. The image represents the EPCAM gene expression in a breast tumour section (Xenium) . a ii , Binary expression of the gene can be visualised, displayed here for EPCAM using a Xenium breast tumour section . b, Example of orientation of H&E image overlay, displayed with coronal mouse Visium brain slice . The Visualiser allows the user to adjust the opacity of the H&E image, displayed with coronal mouse Visium brain slice . c, 3D model overlay. c i , Required inputs for 3D model overlay. 3D-model can be overlayed over single or multiple SRT slides in the Visualiser then aligned and orientated appropriately. c ii , Example of 3D model overlay displayed here with data from the developing human heart . c iii , Accepted file formats for 3D model. c iv , Alignment movements available for 3D model in the Visualiser. d, Selection of ROIs throughout slices and output. d i , User-defined selection of ROIs within 2D slide with option to select same ROI across serial 3D sections or to select up to 4 ROIs within an object. The information of selected ROIs can be exported to csv files then re-imported for subsequent analysis. d ii , Visualisation of clusters in MERFISH adult mouse brain and zoomed individual clusters. When serial slices or 3D objects are available, up to 4 separate ROIs can be selected across serial slices for export allowing subsequent, in-depth analysis. e, Side-by-side comparison. e i , Side-by-side feature allows comparison of two different gene profiles within identical copies of the same section for comparison of marker genes. e ii , Side-by-side comparison displayed using a Xenium breast tumour section . Expression of EPCAM is displayed in the left panel and expression of ELF3 in the right panel. f, After side-by-side comparison has been selected, deselecting this option will ask the user to merge the slides. This creates a comparison of gene expression within the tissue section. Areas with more similar expression between the two genes will be displayed in cool colours, with areas of difference in warm colours. Example data displayed here is Visium human lymph node .

Article Snippet: We envision expanding the AW to include pre-processing pipelines for data from SRT platforms beyond Visium, Xenium and MERFISH (e.g ., Stereopy package for STOmics and a cell segmentation pipeline for image based technologies).

Techniques: Gene Expression, Expressing, Slice Preparation, Selection, Comparison, Marker

Journal: bioRxiv

Article Title: Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics

doi: 10.1101/2023.03.31.535025

Figure Lengend Snippet: a, Visium breast cancer tumour section visualised in VR coloured by regions of high read counts. b, MERFISH adult mouse data displayed in VR, coloured by normalised gene expression with areas of low expression coloured in blue and regions of higher expression in red. Additional information for selected spots will be visualised on the panel on the right-hand side. c, Xenium breast tumour section visualised in VR and coloured by Leiden clustering results. d, Example of 3D object overlay of serial sections in VR for data of human embryonic heart at 6 dpc .

Article Snippet: We envision expanding the AW to include pre-processing pipelines for data from SRT platforms beyond Visium, Xenium and MERFISH (e.g ., Stereopy package for STOmics and a cell segmentation pipeline for image based technologies).

Techniques: Gene Expression, Expressing

Journal: bioRxiv

Article Title: Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics

doi: 10.1101/2023.03.31.535025

Figure Lengend Snippet: a, Benchmarking of 3D-datasets. a i , Data from human embryonic heart at 6 dpc visualised in VR in VR-Omics with spots corresponding to the right ventricle highlighted in red and spots corresponding to the right atrium in blue. a ii , Data from human embryonic heart at 6 dpc aligned and in STich3D. Selection of specific ROIs to highlight the right atrium in black and right ventricle in red performed by a custom R script outside of the STich3D framework. a iii , Example of mouse heart displayed in VR-Cardiomics , right atrium displayed in blue and right ventricle displayed in red. a iv , Metascape results using the differential expressed genes (fold-change>2, FDR-adjusted p-value < 0.05) between the right ventricle and atrium. a v , Radar plot displaying performance of benchmarked tools on performing the following steps: (1) input SRT data; (2) cluster the spots/locations; (3) assemble the slices; (4) manually select two regions of interest (ROIs); (5) generate gene lists to calculate the top differentially expressed genes. b, Comparison of a coronal mouse brain sections generated separately by the b i , Visium and b ii , MERFISH platforms.

Article Snippet: We envision expanding the AW to include pre-processing pipelines for data from SRT platforms beyond Visium, Xenium and MERFISH (e.g ., Stereopy package for STOmics and a cell segmentation pipeline for image based technologies).

Techniques: Selection, Comparison, Generated

Journal: Biomarker Research

Article Title: Single-cell, single-nucleus and xenium-based spatial transcriptomics analyses reveal inflammatory activation and altered cell interactions in the hippocampus in mice with temporal lobe epilepsy

doi: 10.1186/s40364-024-00636-3

Figure Lengend Snippet: Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections. A Whole-brain transcriptomic information obtained through Xenium-based spatial transcriptomics analysis, with reconstructed cell bodies displayed in different colours. The white box highlights the TLE and control hippocampal regions. B Enlarged view of the hippocampal region highlighted in A. C UMAP plot showing the 27 identified cell types. D - I High-resolution expression patterns of marker genes for astrocytes, microglia, oligodendrocytes, CA1 pyramidal neurons, dentate gyrus granule cells, and CA3 pyramidal neurons in Control and TLE sections. The left side represents the brain of a control mouse, while the right side represents the brain of a TLE mouse. Each red dot represents a positive expression point for a gene, with a diameter of 5 μm

Article Snippet: Fig. 6 Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections.

Techniques: Control, Expressing, Marker