A spatial experiment where each row corresponds to a feature and each column corresponds to a spatial location. This file contains pointers to spatial-specific components including the coordinates and image files. Each spatial location is assigned to a sample via a sample_id column in the column data; this is guaranteed to have the same levels as the sample_id values in the image_data property.
Derived from single_cell_experiment/v1.json: a single cell experiment where each row corresponds to a feature and each column corresponds to a single cell. This file contains pointers to single-cell-specific components including reduced dimension results and alternative experiments.
Derived from summarized_experiment/v1.json: a summarized experiment where each row corresponds to a feature and each column corresponds to an experimental sample. The layout of this data structure is based on Bioconductor's SummarizedExperiment class. This metadata document contains pointers to the various components of the summarized experiment, including the row data, column data and assays.
The schema to use.
Is this a child document, only to be interpreted in the context of the parent document from which it is linked? This may have implications for search and metadata requirements.
Path to the file in the project directory.
Array of pointers to alternative experiments. Each file should follow the summarized_experiment schema with number of columns equal to the number of columns in this single cell experiment object.
Name of the alternative experiment. Each alternative experiment should have a non-empty name. Names should be unique across all alternative_experiments.
Must be at least 1 characters long
"CITE-seq"
"spike-ins"
"HTO"
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Name of the main experiment. This should be different from any value in alternative_experiments.name. If omitted, the main experiment is unnamed; if a name is necessary, users are advised to represent the main experiment with an empty string, as this is guaranteed to avoid overlaps with any value in alternative_experiments.name.
"RNA-seq"
Array of pointers to the reduced dimension results. Each entry is expected to follow the array schema, with number of rows equal to the number of columns of the single cell experiment.
Name of the reduced dimensions. Each reduced dimension result should have a non-empty name. Names should be unique across reduced_dimensions.
Must be at least 1 characters long
"PCA"
"TSNE"
"UMAP"
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Pointer to the pixel coordinates for each spatial location, relative to the corresponding image in the image_data.
If type = "point", this is a 2-3 column matrix complying with the hdf5_dense_array schema, where the first column refers to the x-axis, the second column refers to the y-axis, and the third column (if provided) refers to the z-axis. Each row of the matrix corresponds to a column of the spatial experiment.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Type of coordinate.
An array of images for this experiment.
Must contain a minimum of 1 items
Pointer to the actual image file.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
An identifier to distinguish between images for the same sample.
"lowres"
"hires"
Sample of origin for each image. This should match the identifiers in the sample_id column of the column data.
The scaling factor to apply to the coordinates to obtain pixel coordinates on a particular image. This is most relevant when images are downscaled for easier manipulation.
An array of pointers to the assay data. Each entry corresponds to a single assay in the summarized experiment object.
Must contain a minimum of 1 items
Name of the assay. Each assay must have a non-empty name. Assay names should not be duplicated within assays.
Must be at least 1 characters long
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Pointer to the column data. This should be data frame (as defined by the data_frame schema) where each row corresponds to a column of the summarized experiment and each column contains some annotation for the experimental samples. Omitted if no sample-level annotation is present.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Dimensions of a two-dimensional object.
Must contain a minimum of 2 items
Must contain a maximum of 2 items
Pointer to the additional metadata for this object, typically stored as a list (via the basic_list schema). Omitted if no additional metadata is present.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Pointer to the row data. This should be data frame (as defined by the data_frame schema) where each row corresponds to a row of the summarized experiment and each column contains some annotation for the features. Omitted if no feature-level annotation is present.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Pointer to the genomic coordinates corresponding to the rows. This should comply with the genomic_ranges or genomic_ranges_list schemas, where each range or group defines the genomic location of the feature corresponding to a row of the summarized experiment. Omitted if no genomic coordinates are present. This is based on Bioconductor's RangedSummarizedExperiment class.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.