muspan.datasets

The MuSpAn datasets module provides example datasets as MuSpAn domains for testing and demonstration purposes.

Loading in example datasets

load_example_domain

Load an example domain file.

Example datasets

Domain name	Visualisation	Description
Synthetic-Points-Random		A synthetic dataset of points randomly distributed (poisson point process) in a square region. The points have labels ‘Celltype’ with four categories: ‘A’, ‘B’, ‘C’, ‘D’ equally distributed.
Synthetic-Points-Aggregation		A synthetic dataset of points in aggregated clusters in a square region. The points have labels ‘Celltype’ with four categories: ‘A’, ‘B’, ‘C’, ‘D’. Points with labels ‘A’, ‘B’ and ‘C’ are aggregated in clusters, while points with label ‘D’ are randomly distributed (poisson point process).
Synthetic-Points-Exclusion		A synthetic dataset of points defining a region of exclusion in a square region. The points have labels ‘Celltype’ with four categories: ‘A’, ‘B’, ‘C’, ‘D’. Points with labels ‘A’, ‘B’ and ‘D’ are aggregated in central region with label ‘C’ points excluded from this region.
Synthetic-Points-Architecture		A synthetic dataset of points with different spatial architectures in a square region. The points have labels ‘Celltype’ with four categories: ‘A’, ‘B’, ‘C’, ‘D’. Points with labels ‘A’ and ‘B’ form small regular annulus structures. Points in label ‘C’ form a large circle structure. Points in label ‘D’ are randomly distributed (poisson point process).
Xenium-Healthy-Colon		A selected ROI from a sample of healthy colon tissue from a 10x Xenium dataset provided in the public resources repository, see link. The domain contains cell boundaries, nuclei and a selection of transcripts: Mylk, Myl9, Cnn1, Mgll, Mustn1, Oit1, Cldn2, Nupr1, Sox9, Ccl9. The dataset also contains cell clustering labels produced by Xenium Onboard Analysis using the ‘Graph-based’ method. This dataset is licensed under the Creative Commons Attribution license.
Macrophage-Hypoxia-ROI		A 1.5mm square region of interest formed from a stack of aligned IHC slides in a human head and neck cancer image, see link. The domain contains cell centre locations of macrophages (CD68+), and shapes which denote boundaries of PanCK (a tumour marker), CAIX (a marker for hypoxia) and Pimonidazole (a marker for severe hypoxia).
Mouse-Colon-Carcinoma		A 1mm square image of mouse colorectal carcinoma containing 5 different immune markers and one epithelial marker. This dataset was used the paper Extended correlation functions for spatial analysis of multiplex imaging data.