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spatial datasets

Repository of spatial datasets analyzed by Giotto. Each dataset has its own folder with subfolders for:

  • count matrix
  • locations
  • giotto R-script with secondary analyis (when available)
  • raw data (optional)

These datasets can be downloaded directly from within the Giotto package using the function getSpatialDataset as illustrated in the examples.

Visium datasets are not available, but the original directory can be downloaded from the 10X Visium website and directly used as input for the wrapper createGiottoVisiumObject to create a Giotto object.

Available datasets

2023

Spatial Genomics Mouse Kidney Mini Dataset

  • website

2022

Molecular Cartography Human Lung

single-cell Human Prostate

single-cell Mouse Brain


2020

Spatial Transcriptomics squamous cell carcinoma


2019

Visium kidney

Visium brain

merFISH

seqFISH+ somatosensory cortex

seqFISH+ olfactory bulb

slide-seq cerebellum


2018

STARmap 3D cortex

osmFISH somatosensory cortex

merFISH 3D hypothalamic preoptic region

CODEX spleen

CyCIF PDAC

MIBI TNBC


2016

Spatial Transcriptomics olfactory bulb

Soon available datasets

  1. slide-seq
  2. MIBI
  3. ...