Use Case Gallery

How scientists turn complex spatial multi-omics data into biological insights.

Spatial transcriptomics

10x Visium

Spatial domain mapping

Human Lymph Node (Space Ranger 1.1.0)

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Spatial transcriptomics

10x Visium HD

Spatially variable genes

Human lung cancer (FFPE), immunofluorescence-stained section

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Spatial transcriptomics

10x Xenium

Single-cell spatial typing on H&E

Human lung cancer (FFPE), 289-gene lung panel, with H&E of the same section

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Spatial transcriptomics

Bruker CosMx

Cell typing across a tissue microarray

Colorectal cancer tissue microarray (MSI and MSS tumors with normal mucosa), 1,000-plex RNA panel

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Spatial transcriptomics

Vizgen MERSCOPE

Tumor microenvironment composition

Human ovarian cancer, 316-gene immuno-oncology panel

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Spatial transcriptomics

Bruker GeoMx DSP

Differential expression between tissue compartments

Human kidney biopsies, minimal change disease vs controls (GSE277674)

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Spatial proteomics

Akoya PhenoCycler (CODEX)

Cell neighborhood analysis

Normal human bone marrow, 54-marker PhenoCycler-Fusion scan (H36)

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Spatial proteomics

Akoya Vectra QPTIFF

Marker positivity and threshold sensitivity

LuCa-7color whole-slide scan, original Vectra Polaris file

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Spatial proteomics

Multiplex IF (OME-TIFF)

Channel phenotypes and neighborhoods

LuCa-7color whole-slide scan (Vectra Polaris)

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Spatial proteomics

Imaging mass cytometry

Imaging mass cytometry cell phenotyping

Example imaging mass cytometry raw data, patient 1

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10x Chromium

scRNA-seq cell annotation

10k PBMCs from a healthy donor (v3 chemistry)

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AnnData .h5ad

Checking curated cell labels

Immune cells from SCLC patients (Ng et al. 2026, Cancer Cell)

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cBioPortal mutations

Mutation co-occurrence analysis

TCGA lung adenocarcinoma, PanCancer Atlas: 566 sequenced tumors

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Aperio SVS

Tissue and nuclei quantification

TCGA-AR-A0TX diagnostic H&E slide (TCGA-BRCA)

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Hamamatsu NDPI

Nuclei density on H&E

Hamamatsu-2: H&E section scanned on a Hamamatsu NanoZoomer

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Philips TIFF

Lymph node cellularity

Philips-1: lymph node H&E from CAMELYON16

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Zeiss CZI

Nuclei counting on trichrome

Zeiss-5: mouse kidney, trichrome stain, two scenes

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Leica SCN

Nuclei density across sections

Leica-2: mouse kidney H&E, four sections scanned as separate 40× regions

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