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lung cancer research immune network technology data analysis clinical application spatial transcriptomics • merfish  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc lung cancer research immune network technology data analysis clinical application spatial transcriptomics • merfish
    Lung Cancer Research Immune Network Technology Data Analysis Clinical Application Spatial Transcriptomics • Merfish, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/analysis+spatial+transcriptomics/merfish/pm41619173-675-24-34
    Average 86 stars, based on 1 article reviews
    lung cancer research immune network technology data analysis clinical application spatial transcriptomics • merfish - by Bioz Stars, 2026-10
    86/100 stars

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    Related Articles

    Spatial Transcriptomics:

    Article Title: The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.
    Article Snippet: .. D ow nloaded from https://academ ic.oup.com /gpb/advance-article/doi/10.1093/gpbjnl/qzag010/8450248 by guest on 04 February 2026 The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research Immune Network Technology Data Analysis Clinical Application Spatial Transcriptomics • MERFISH, Xenium • FISSEQ • Visium, Stereo-seq Spatial Proteomics • IMC, MIBI • CODEX, CosMx Emerging • Spatial Metabolomics • Spatial Epigenomics Image Processing & Segmentation Annotation Cross-modal Fusion Normalization Cell-cell CommunicationVisualization Biopsy Precision Treatment Margin, Core, Stroma, Nest Spaial Structure Subtpye Heterogeneity Tumor Architecture Im une Int ractions Future Outlook Enhance Technical Performance • Higher Resolution • Higher Input • Larger Area Spatiotemporal Data FusionPatient 1 Patient n Tumor ... • Different Technology • Different Sampling Location • Different Sampling Time • Lower prices • Less time Standardization Scalability Graphic Abstract Click here to access/download;Figure;Graphic Abstract.pdf D ow nloaded from https://academ ic.oup.com /gpb/advance-article/doi/10.1093/gpbjnl/qzag010/8450248 by guest on 04 February 2026 ..

    Article Title: SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets
    Article Snippet: .. Image-based spatial transcriptomics technologies that utilize fluorescence in situ hybridization or in situ sequencing, such as seqFISH+ , osmFISH , MERFISH , and STARmap , can offer single-cell resolution expression and precise spatial information of RNA transcripts. .. These methods utilize pre-designed probes and high-resolution microscopy for detection, thus enabling absolute quantification of transcripts with spatial context, but they are restricted to limited pre-selected genes compared to sequencing-based spatial transcriptomics technologies.

    Article Title: MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart
    Article Snippet: .. Together, these improvements make MERFISH+ probes a more robust and reliable platform for high-resolution spatial transcriptomics, especially for limited human samples. ..

    Article Title: NicheAgent: LLM-Guided Zero-Shot Niche Identification for Spatial Transcriptomics
    Article Snippet: .. Spatial transcriptomics (ST) technologiesincluding MERFISH [ ], STARmap [ ], and 10x Visium enable in situ measurement of gene expression while preserving the native spatial organization of tissues. ..

    Article Title: Nicheformer: a foundation model for single-cell and spatial omics
    Article Snippet: .. The spatial part of the SpatialCorpus-110M consists of datasets measured with image-based spatial transcriptomics technologies, namely CosMx, ISS, MERFISH and 10x Xenium. ..

    Article Title: SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics
    Article Snippet: .. Spatial transcriptomics technologies such as Xenium, MERFISH, and Visium HD enable high-resolution profiling of gene expression while preserving tissue architecture. ..

    Spatial Proteomics:

    Article Title: The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.
    Article Snippet: .. D ow nloaded from https://academ ic.oup.com /gpb/advance-article/doi/10.1093/gpbjnl/qzag010/8450248 by guest on 04 February 2026 The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research Immune Network Technology Data Analysis Clinical Application Spatial Transcriptomics • MERFISH, Xenium • FISSEQ • Visium, Stereo-seq Spatial Proteomics • IMC, MIBI • CODEX, CosMx Emerging • Spatial Metabolomics • Spatial Epigenomics Image Processing & Segmentation Annotation Cross-modal Fusion Normalization Cell-cell CommunicationVisualization Biopsy Precision Treatment Margin, Core, Stroma, Nest Spaial Structure Subtpye Heterogeneity Tumor Architecture Im une Int ractions Future Outlook Enhance Technical Performance • Higher Resolution • Higher Input • Larger Area Spatiotemporal Data FusionPatient 1 Patient n Tumor ... • Different Technology • Different Sampling Location • Different Sampling Time • Lower prices • Less time Standardization Scalability Graphic Abstract Click here to access/download;Figure;Graphic Abstract.pdf D ow nloaded from https://academ ic.oup.com /gpb/advance-article/doi/10.1093/gpbjnl/qzag010/8450248 by guest on 04 February 2026 ..

    Sampling:

    Article Title: The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.
    Article Snippet: .. D ow nloaded from https://academ ic.oup.com /gpb/advance-article/doi/10.1093/gpbjnl/qzag010/8450248 by guest on 04 February 2026 The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research Immune Network Technology Data Analysis Clinical Application Spatial Transcriptomics • MERFISH, Xenium • FISSEQ • Visium, Stereo-seq Spatial Proteomics • IMC, MIBI • CODEX, CosMx Emerging • Spatial Metabolomics • Spatial Epigenomics Image Processing & Segmentation Annotation Cross-modal Fusion Normalization Cell-cell CommunicationVisualization Biopsy Precision Treatment Margin, Core, Stroma, Nest Spaial Structure Subtpye Heterogeneity Tumor Architecture Im une Int ractions Future Outlook Enhance Technical Performance • Higher Resolution • Higher Input • Larger Area Spatiotemporal Data FusionPatient 1 Patient n Tumor ... • Different Technology • Different Sampling Location • Different Sampling Time • Lower prices • Less time Standardization Scalability Graphic Abstract Click here to access/download;Figure;Graphic Abstract.pdf D ow nloaded from https://academ ic.oup.com /gpb/advance-article/doi/10.1093/gpbjnl/qzag010/8450248 by guest on 04 February 2026 ..

    Fluorescence:

    Article Title: SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets
    Article Snippet: .. Image-based spatial transcriptomics technologies that utilize fluorescence in situ hybridization or in situ sequencing, such as seqFISH+ , osmFISH , MERFISH , and STARmap , can offer single-cell resolution expression and precise spatial information of RNA transcripts. .. These methods utilize pre-designed probes and high-resolution microscopy for detection, thus enabling absolute quantification of transcripts with spatial context, but they are restricted to limited pre-selected genes compared to sequencing-based spatial transcriptomics technologies.

    Article Title: Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology.
    Article Snippet: .. Spatial transcriptomics platforms such as 10× Visium, Slide-seq, and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) preserve tissue architecture while capturing spatially resolved gene expression profiles, enabling the identification of spatial gradients in inflammatory signaling, revascularization, and epidermal regeneration [66,67]. ..

    In Situ Hybridization:

    Article Title: SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets
    Article Snippet: .. Image-based spatial transcriptomics technologies that utilize fluorescence in situ hybridization or in situ sequencing, such as seqFISH+ , osmFISH , MERFISH , and STARmap , can offer single-cell resolution expression and precise spatial information of RNA transcripts. .. These methods utilize pre-designed probes and high-resolution microscopy for detection, thus enabling absolute quantification of transcripts with spatial context, but they are restricted to limited pre-selected genes compared to sequencing-based spatial transcriptomics technologies.

    Article Title: Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology.
    Article Snippet: .. Spatial transcriptomics platforms such as 10× Visium, Slide-seq, and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) preserve tissue architecture while capturing spatially resolved gene expression profiles, enabling the identification of spatial gradients in inflammatory signaling, revascularization, and epidermal regeneration [66,67]. ..

    In Situ:

    Article Title: SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets
    Article Snippet: .. Image-based spatial transcriptomics technologies that utilize fluorescence in situ hybridization or in situ sequencing, such as seqFISH+ , osmFISH , MERFISH , and STARmap , can offer single-cell resolution expression and precise spatial information of RNA transcripts. .. These methods utilize pre-designed probes and high-resolution microscopy for detection, thus enabling absolute quantification of transcripts with spatial context, but they are restricted to limited pre-selected genes compared to sequencing-based spatial transcriptomics technologies.

    Article Title: NicheAgent: LLM-Guided Zero-Shot Niche Identification for Spatial Transcriptomics
    Article Snippet: .. Spatial transcriptomics (ST) technologiesincluding MERFISH [ ], STARmap [ ], and 10x Visium enable in situ measurement of gene expression while preserving the native spatial organization of tissues. ..

    Sequencing:

    Article Title: SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets
    Article Snippet: .. Image-based spatial transcriptomics technologies that utilize fluorescence in situ hybridization or in situ sequencing, such as seqFISH+ , osmFISH , MERFISH , and STARmap , can offer single-cell resolution expression and precise spatial information of RNA transcripts. .. These methods utilize pre-designed probes and high-resolution microscopy for detection, thus enabling absolute quantification of transcripts with spatial context, but they are restricted to limited pre-selected genes compared to sequencing-based spatial transcriptomics technologies.

    Single Cell:

    Article Title: SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets
    Article Snippet: .. Image-based spatial transcriptomics technologies that utilize fluorescence in situ hybridization or in situ sequencing, such as seqFISH+ , osmFISH , MERFISH , and STARmap , can offer single-cell resolution expression and precise spatial information of RNA transcripts. .. These methods utilize pre-designed probes and high-resolution microscopy for detection, thus enabling absolute quantification of transcripts with spatial context, but they are restricted to limited pre-selected genes compared to sequencing-based spatial transcriptomics technologies.

    Expressing:

    Article Title: SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets
    Article Snippet: .. Image-based spatial transcriptomics technologies that utilize fluorescence in situ hybridization or in situ sequencing, such as seqFISH+ , osmFISH , MERFISH , and STARmap , can offer single-cell resolution expression and precise spatial information of RNA transcripts. .. These methods utilize pre-designed probes and high-resolution microscopy for detection, thus enabling absolute quantification of transcripts with spatial context, but they are restricted to limited pre-selected genes compared to sequencing-based spatial transcriptomics technologies.

    Gene Expression:

    Article Title: NicheAgent: LLM-Guided Zero-Shot Niche Identification for Spatial Transcriptomics
    Article Snippet: .. Spatial transcriptomics (ST) technologiesincluding MERFISH [ ], STARmap [ ], and 10x Visium enable in situ measurement of gene expression while preserving the native spatial organization of tissues. ..

    Article Title: SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics
    Article Snippet: .. Spatial transcriptomics technologies such as Xenium, MERFISH, and Visium HD enable high-resolution profiling of gene expression while preserving tissue architecture. ..

    Article Title: Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology.
    Article Snippet: .. Spatial transcriptomics platforms such as 10× Visium, Slide-seq, and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) preserve tissue architecture while capturing spatially resolved gene expression profiles, enabling the identification of spatial gradients in inflammatory signaling, revascularization, and epidermal regeneration [66,67]. ..

    Preserving:

    Article Title: NicheAgent: LLM-Guided Zero-Shot Niche Identification for Spatial Transcriptomics
    Article Snippet: .. Spatial transcriptomics (ST) technologiesincluding MERFISH [ ], STARmap [ ], and 10x Visium enable in situ measurement of gene expression while preserving the native spatial organization of tissues. ..

    Article Title: SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics
    Article Snippet: .. Spatial transcriptomics technologies such as Xenium, MERFISH, and Visium HD enable high-resolution profiling of gene expression while preserving tissue architecture. ..

    Generated:

    Article Title: A spatially informed matrix normal model for gene co-expression analysis in spatial transcriptomics studies
    Article Snippet: .. We conducted a cross-species gene co-expression analysis on human and mouse brain cortex data [ ] generated by MERFISH, an imaging-based spatial transcriptomics technology [ ]. ..

    Imaging:

    Article Title: A spatially informed matrix normal model for gene co-expression analysis in spatial transcriptomics studies
    Article Snippet: .. We conducted a cross-species gene co-expression analysis on human and mouse brain cortex data [ ] generated by MERFISH, an imaging-based spatial transcriptomics technology [ ]. ..



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    10X Genomics spatial transcriptomic analysis
    a Schematic diagram of the spatial <t>transcriptome</t> analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.
    Spatial Transcriptomic Analysis, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    spatial transcriptomic analysis - by Bioz Stars, 2026-10
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    spatial transcriptomics data analysis  (Spatial Transcriptomics Inc)
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    Spatial Transcriptomics Inc spatial transcriptomics data analysis
    a Schematic diagram of the spatial <t>transcriptome</t> analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.
    Spatial Transcriptomics Data Analysis, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/analysis+spatial+transcriptomics/rna+seq/pm41508250-90-0-0
    Average 86 stars, based on 1 article reviews
    spatial transcriptomics data analysis - by Bioz Stars, 2026-10
    86/100 stars
    		  Buy from Supplier

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    a Schematic diagram of the spatial transcriptome analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.

    Journal: bioRxiv

    Article Title: CXCL10 drives female-specific tau pathology progression and defines sex-dependent vulnerability in tauopathy model mice

    doi: 10.64898/2026.04.19.719088

    Figure Lengend Snippet: a Schematic diagram of the spatial transcriptome analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.

    Article Snippet: FFPE brain sections were analyzed using Xenium spatial transcriptome analysis (10x Genomics).

    Techniques: Formalin-fixed Paraffin-Embedded, Olfactory, Gene Expression