Gallery

Human lung cancer (Xenium)

H&E and morphology images, cell and nucleus segmentation, 12.2M transcripts and cell boundaries, read from a SpatialData store.

• Xenium
• SpatialData
• OME-Zarr
• Parquet

Data: 10x Genomics, CC BY 4.0

LuCa 7-color multiplex scan

Multiplex immunofluorescence whole-slide scan (DAPI, FITC, CY3, Texas Red, CY5), opened directly from the 2 GB QPTIFF file.

• Multiplex IF
• QPTIFF

Data: PerkinElmer (now Akoya), via the OME sample images, CC BY 4.0, © PerkinElmer

Points2Regions

Fast, interactive clustering of imaging-based spatial transcriptomics data, as a TissUUmaps plugin. Try it on human heart, mouse brain or your own data.

• In situ sequencing
• Clustering
• Plugin

DEPICTER

Deep representation clustering for histology annotation, shown on a whole-slide image of the CAMELYON17 dataset.

• Histology
• H&E
• Deep learning

Developmental human heart

De novo modelling of cell-type signatures in the developing human heart, from in situ sequencing data analysed with spage2vec.

• In situ sequencing
• Cell typing

Human Developmental Lung Cell Atlas

Single-cell RNA sequencing, in situ sequencing, SCRINSHOT and Spatial Transcriptomics of the developing human lung, from 5 to 14 post-conception weeks.

• scRNA-seq
• In situ sequencing
• SCRINSHOT
• Spatial Transcriptomics

Mouse brain compartments

Spatial compartments of the mouse brain, identified automatically from in situ sequencing data, on four sections.

• In situ sequencing
• Clustering

Spage2vec

Unsupervised representation of localized spatial gene expression signatures, on in situ sequencing, osmFISH and MERFISH data.

• In situ sequencing
• osmFISH
• MERFISH

Prostate cancer grading

Full-resolution digitized prostate biopsies with AI-based detection, localisation and Gleason grading of prostate cancer.

• Histology
• H&E
• Deep learning