LoadAteraSegmentations

<code>LoadAtera(..., segmentations = "cell")</code> builds a <code>Polygons</code>
object (via <code><a href="https://edzer.github.io/sp/reference/SpatialPolygons.html">sp::SpatialPolygons()</a></code>) for every cell up front, which
doesn't scale to bundles with many hundreds of thousands of cells -- that
machinery gets impractically slow, and can overflow R's protection stack,
well before reaching cell counts typical of a whole-tissue Atera run. This
function instead builds segmentation polygons only for the cells already
present in <code>object[[fov]]</code>, so a bundle too large to load
segmentations for up front (<code>LoadAtera(..., segmentations = NULL)</code>)
can still get polygons for a <code>Crop</code>ped
region-of-interest FOV, which typically has orders of magnitude fewer
cells.

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. 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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331>, Jiang, et al (2026) for more details.

Paul Hoffman

Seurat

Tools for Single Cell Genomics

Andrew Butler

Saket Choudhary

David Collins

Charlotte Darby

Jeff Farrell

Isabella Grabski

Christoph Hafemeister

Yuhan Hao

Austin Hartman

Jaison Jain

Longda Jiang

Madeline Kowalski

Skylar Li

Gesmira Molla

Efthymia Papalexi

Patrick Roelli

Rahul Satija

Karthik Shekhar

Anagha Shenoy

Avi Srivastava

Tim Stuart

Kristof Torkenczy

Brian Zhang

Shiwei Zheng

Satija Lab and Collaborators 

LoadAteraSegmentations function

<dl><dt>object</dt>
<dd>A Seurat object created by <code>LoadAtera</code></dd>
<dt>data.dir</dt>
<dd>The same <code>data.dir</code> passed to the original
<code>LoadAtera</code> call (the Atera output bundle directory)</dd>
<dt>fov</dt>
<dd>Name of the FOV (typically already cropped via
<code>Crop</code>) to add segmentation polygons to</dd>
<dt>segmentations</dt>
<dd>One of <code>"cell"</code> or <code>"nucleus"</code></dd></dl>

Arguments

<code>LoadAtera(..., segmentations = "cell")</code> builds a <code>Polygons</code>
object (via <code><a href='https://edzer.github.io/sp/reference/SpatialPolygons.html'>sp::SpatialPolygons()</a></code>) for every cell up front, which
doesn't scale to bundles with many hundreds of thousands of cells -- that
machinery gets impractically slow, and can overflow R's protection stack,
well before reaching cell counts typical of a whole-tissue Atera run. This
function instead builds segmentation polygons only for the cells already
present in <code>object[[fov]]</code>, so a bundle too large to load
segmentations for up front (<code>LoadAtera(..., segmentations = NULL)</code>)
can still get polygons for a <code>Crop</code>ped
region-of-interest FOV, which typically has orders of magnitude fewer
cells.

Add segmentation polygons to an Atera field of view, for only the cells
currently present in it — LoadAteraSegmentations

<dl>

<dt>object</dt>
<dd>A Seurat object created by <code>LoadAtera</code></dd>


<dt>data.dir</dt>
<dd>The same <code>data.dir</code> passed to the original
<code>LoadAtera</code> call (the Atera output bundle directory)</dd>


<dt>fov</dt>
<dd>Name of the FOV (typically already cropped via
<code>Crop</code>) to add segmentation polygons to</dd>


<dt>segmentations</dt>
<dd>One of <code>"cell"</code> or <code>"nucleus"</code></dd>

</dl>

Add segmentation polygons to an Atera field of view, for only the cells
currently present in it

LoadAteraSegmentations: Add segmentation polygons to an Atera field of view, for only the cells currently present in it

Description

Usage

Value

Arguments