SpatialImage-class

SpatialImage

The <code>SpatialImage</code> class is a virtual class representing spatial
information for Seurat. All spatial image information must inherit from this
class for use with <code>Seurat</code> objects

Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. See
Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>,
Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>,
Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
more details.

Paul Hoffman

SeuratObject

Data Structures for Single Cell Data

Rahul Satija

David Collins

Yuhan Hao

Austin Hartman

Gesmira Molla

Andrew Butler

Tim Stuart

Madeline Kowalski

Saket Choudhary

Skylar Li

Longda Jiang

Anagha Shenoy

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

SpatialImage-class function

<dl>
<dt><code>assay</code></dt>
<dd>Name of assay to associate image data with; will give this image
priority for visualization when the assay is set as the active/default assay
in a <code>Seurat</code> object</dd></dl>
<dt><code>key</code></dt>
<dd>A one-length character vector with the object's key; keys must
be one or more alphanumeric characters followed by an underscore
&#8220;<code>_</code>&#8221; (regex pattern
&#8220;<code>SeuratObject:::.KeyPattern()</code>&#8221;)</dd>
<dt><code>misc</code></dt>
<dd>A named list of unstructured miscellaneous data</dd>

Slots

The SpatialImage class — SpatialImage-class

<dl>
<dt><code>assay</code></dt>
<dd>Name of assay to associate image data with; will give this image
priority for visualization when the assay is set as the active/default assay
in a <code>Seurat</code> object</dd>


<dt><code>key</code></dt>
<dd>A one-length character vector with the object's key; keys must
be one or more alphanumeric characters followed by an underscore
&#8220;<code>_</code>&#8221; (regex pattern
&#8220;<code>SeuratObject:::.KeyPattern()</code>&#8221;)</dd>


<dt><code>misc</code></dt>
<dd>A named list of unstructured miscellaneous data</dd>


</dl>

The SpatialImage class

SpatialImage-class: The SpatialImage class

Description

Arguments

Slots

See Also