DamondPancreas2019: Deprecated function - 'DamondPancreas2019' dataset

DamondPancreas2019R Documentation

Deprecated function - 'DamondPancreas2019' dataset

Description

These functions are provided for compatibility with older versions of ‘imcdatasets’ only, and will be defunct at the next release. This dataset consists of three data objects: single cell data, multichannel images and cell segmentation masks. The data was obtained by imaging mass cytometry of human pancreas sections from donors with type 1 diabetes.

Usage

DamondPancreas2019_sce(metadata = FALSE)
DamondPancreas2019_images(metadata = FALSE)
DamondPancreas2019_masks(metadata = FALSE)

Arguments

metadata

logical value indicating whether ExperimentHub metadata (describing the overall dataset) should be returned only, or if the whole dataset should be loaded. Default = FALSE, which loads the whole dataset.

Details

This is an Imaging Mass Cytometry (IMC) dataset from Damond et al. (2019), consisting of three data objects. Note: The following functions are deprecated and will be made defunct; use the replacements indicated below:

  • DamondPancreas2019_images -> DamondPancreas2019Data contains a hundred 38-channel images in the form of a CytoImageList class object.

  • DamondPancreas2019_masks -> DamondPancreas2019Data contains the cell segmentation masks associated with the images, in the form of a CytoImageList class object.

  • DamondPancreas2019_sce -> DamondPancreas2019Data contains the single cell data extracted from the images using the cell segmentation masks, as well as the associated metadata, in the form of a SingleCellExperiment. This represents a total of 252,059 cells x 38 channels.

All data are downloaded from ExperimentHub and cached for local re-use.

Mapping between the three data objects is performed via variables located in their metadata columns: mcols() for the CytoImageList objects and ColData() for the SingleCellExperiment object. Mapping at the image level can be performed with the ImageName or ImageNumber variables. Mapping between cell segmentation masks and single cell data is performed with the CellNumber variable, the values of which correspond to the intensity values of the DamondPancreas2019_masks object. For practical examples, please refer to the "Accessing IMC datasets" vignette.

This dataset is a subset of the complete Damond et al. (2019) dataset comprising the data from three pancreas donors at different stages of type 1 diabetes (T1D). The three donors present clearly diverging characteristics in terms of cell type composition and cell-cell interactions, which makes this dataset ideal for benchmarking spatial and neighborhood analysis algorithms.

The assay slot of the SingleCellExperiment object contains two assays:

  • counts contains mean ion counts per cell.

  • exprs contains arsinh-transformed counts, with cofactor 1.

The marker-associated metadata, including antibody information and metal tags are stored in the rowData of the SingleCellExperiment object.

The cell-associated metadata are stored in the colData of the SingleCellExperiment object. These metadata include cell types (in colData(sce)$CellType) and broader cell categories, such as "immune" or "islet" cells (in colData(sce)$CellCat). In addition, for cells located inside pancreatic islets, the islet they belong to is indicated in colData(sce)$ParentIslet. For cells not located in islets, the "ParentIslet" value is set to 0 but the spatially closest islet can be identified with colData(sce)$ClosestIslet.

The donor-associated metadata are also stored in the colData of the SingleCellExperiment object. For instance, the donors' IDs can be retrieved with colData(sce)$case and the donors' disease stage can be obtained with colData(sce)$stage.

The three donors present the following characteristics:

  • 6126 is a non-diabetic donor, with large islets containing many beta cells, severe infiltration of the exocrine pancreas with myeloid cells but limited infiltration of islets.

  • 6414 is a donor with recent T1D onset (shortly after diagnosis) showing partial beta cell destruction and mild infiltration of islets with T cells.

  • 6180 is a donor with long-duration T1D (11 years after diagnosis), showing near-total beta cell destruction and limited immune cell infiltration in both the islets and the pancreas.

File sizes:

  • `images`: size in memory = 7.4 Gb, size on disk = 1780 Mb.

  • `masks`: size in memory = 200.0 Mb, size on disk = 8.6 Mb.

  • `sce`: size in memory = 248.6 Mb, size on disk = 145 Mb.

Original source: Damond et al. (2019): https://doi.org/10.1016/j.cmet.2018.11.014

Original link to raw data, also containing the entire dataset: https://data.mendeley.com/datasets/cydmwsfztj/2

Value

Returns a SingleCellExperiment or CytoImageList object.

Author(s)

Nicolas Damond

Source

Publication Original dataset

References

Damond N et al. (2019). A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry. Cell Metab 29(3), 755-768.

Examples

sce <- DamondPancreas2019Data(data_type = "sce")
sce
images <- DamondPancreas2019Data(data_type = "images")
head(images)
masks <- DamondPancreas2019Data(data_type = "masks")
head(masks)

BodenmillerGroup/imcdatasets documentation built on July 5, 2022, 4:34 p.m.