ManualAlignImages: Manual alignment of images

In jbergenstrahle/STUtility: Analysis and visualization of Spatial Transcriptomics data

Manual alignment of images

Description

Creates an interactive shiny application to align images manually

Usage

ManualAlignImages(
  object,
  type = NULL,
  reference.index = 1,
  edges = TRUE,
  verbose = FALSE,
  limit = 0.3,
  maxnum = 1000,
  fix.axes = FALSE,
  custom.edge.detector = NULL
)

## S3 method for class 'Staffli'
ManualAlignImages(
  object,
  type = "masked.masks",
  reference.index = 1,
  edges = TRUE,
  verbose = FALSE,
  limit = 0.3,
  maxnum = 1000,
  fix.axes = FALSE,
  custom.edge.detector = NULL
)

## S3 method for class 'Seurat'
ManualAlignImages(
  object,
  type = "masked.masks",
  reference.index = 1,
  edges = TRUE,
  verbose = FALSE,
  limit = 0.3,
  maxnum = 1000,
  fix.axes = FALSE,
  custom.edge.detector = NULL
)

Arguments

object	Seurat object
type	Image type to use as input for alignment [default: 'masked.masks']
reference.index	Specifies reference sample image for alignment [default: 1]
edges	Uses the tissue edges for alignment
verbose	Print messages
limit	Pixel intensity limit for thresholding
maxnum	Maximum number of points to display in the app
fix.axes	Fix axes of images
custom.edge.detector	Custom function used to detect edges in tissue image. If a function is provided, the edges option will be overridden.

Value

A Staffli object

A Seurat object

Examples

## Not run: 
# Create a new Staffli object, mask, align and plot images (will start an interactive shiny session)
st.obj <- CreateStaffliObject(imgs, meta.data)
st.obj <- LoadImages(st.obj, verbose = TRUE) %>% MaskImages() %>% ManualAlignImages()
plot(st.obj)

## End(Not run)
## Not run: 
# Load, mask, align and plot images (will start an interactive shiny session)
se <- LoadImages(se, verbose = TRUE) %>% MaskImages() %>% ManualAlignImages()
ImagePlot(se)

## End(Not run)

jbergenstrahle/STUtility documentation built on March 14, 2023, 7:15 a.m.