Apply rigid transformations to images

Usage

RigidTransformImages(object, ...)

# S3 method for default
RigidTransformImages(object, image, xy_coords, verbose = TRUE, ...)

# S3 method for Seurat
RigidTransformImages(object, transforms, verbose = TRUE, ...)

Arguments

object: An object
...: Arguments passed to other methods
image: An image of class magick-image, raster, StoredSpatialImage or a path to an image in PNG or JPEG format
xy_coords: Spot coordinates that can be mapped to image
verbose: Print messages
transforms: a tibble containing information about the transformations to apply to the images (see Seurat section)

Value

A list with two elements:

"im_transf": An object of class magick-image representing the transformed image
"xy_transf": An object of class tbl representing the transformed coordinates

default method

Object is a tibble containing information about the image dimensions that are matched with xy_coords. The coordinates xy_coords do not have to match the input image as long as the image dimensions in object are matched. This is to ensure that the coordinates can be transformed correctly regardless of the dimensions of the image. For example, the coordinates provided by spaceranger in "tissue_positions.csv" can be mapped to the original H&E image and therefore the original H&E image dimensions are required to correctly specify the dimensions when using these coordinates for plotting. Doing so, we can map the coordinates correctly on the H&E image regardless of its size.

The required columns are:

full_width, full_height: the dimensions of the image that xy_coords map to
sampleID: an integer specifying a sample ID
mirror_x, mirror_y: TRUE/FALSE specifying if the image should be mirrored along the x- and/or y-axis
angle: a numeric specifying an angle to rotate the image by in degrees
tr_x, tr_y: numeric values specifying translations along the x- and/or y-axis. tr_x, tr_y have to be values between -1 and 1 where 0 means no translation and 1 is equal to the image width or height. Negative values will shift the image along the axis in the opposite direction. For example, setting tr_x = 0.5 will move the image 50 to the right and setting tr_x = -0.5 will move the image 50

Author

Ludvig Larsson

Examples


library(semla)
library(tibble)
library(dplyr)
library(magick)
library(patchwork)
library(ggplot2)

transforms <- generate_rigid_transform(mirror_x = TRUE, angle = 30, tr_x = 0.2, tr_y = -0.2)

# Combine image dimensions with transforms.
# These are the dimensions of the H&E image used as input for
# spaceranger count.
transforms <- tibble(full_width = 18107, full_height = 19242) |>
  bind_cols(transforms)
transforms
#> # A tibble: 1 × 9
#>   full_width full_height sampleID mirror_x mirror_y angle  tr_x  tr_y
#>        <dbl>       <dbl>    <dbl> <lgl>    <lgl>    <dbl> <dbl> <dbl>
#> 1      18107       19242        1 TRUE     FALSE       30   0.2  -0.2
#> # ℹ 1 more variable: scalefactor <dbl>
# get example coordinate file
coordinatefile <- system.file("extdata/mousebrain/spatial",
                              "tissue_positions_list.csv",
                              package = "semla")

# Load coordinates
# These coordinates are defined on the H&E image used as input for
# spaceranger count.
xy <- LoadSpatialCoordinates(coordinatefiles = coordinatefile)
#> ℹ Loading coordinates:
#> →   Finished loading coordinates for sample 1
#> ℹ Collected coordinates for 2560 spots.
xy
#> # A tibble: 2,560 × 7
#>    barcode   selected     y     x pxl_row_in_fullres pxl_col_in_fullres sampleID
#>    <chr>        <int> <int> <int>              <int>              <int>    <int>
#>  1 CATACAAA…        1    13    35               4117               6086        1
#>  2 CTGAGCAA…        1    15    25               4472               5062        1
#>  3 GGGTACCC…        1    14    26               4294               5164        1
#>  4 ACGGAATT…        1    15    27               4472               5266        1
#>  5 GGGCGGTC…        1    14    28               4294               5369        1
#>  6 ATGTTACG…        1    15    29               4472               5471        1
#>  7 AACCATGG…        1    14    30               4294               5574        1
#>  8 TCGCATCC…        1    15    31               4473               5676        1
#>  9 ACTTAGTA…        1    14    32               4295               5778        1
#> 10 GAGCTCTC…        1    15    33               4473               5881        1
#> # ℹ 2,550 more rows

# Load image
lowresimagefile <- system.file("extdata/mousebrain/spatial",
                               "tissue_lowres_image.jpg",
                               package = "semla")
im <- image_read(lowresimagefile)

# Transform image and coordinates
transf_res <- RigidTransformImages(transforms, image = im, xy_coords = xy)
#> ℹ Fetched spot coordinates
#> ℹ Supplied transformations are valid
#> →   Mirror along x-axis: TRUE
#> →   Mirror along y-axis: FALSE
#> →   Rotation angle: 30
#> →   Translation along x axis: 20%
#> →   Translation along y axis: -20%
#> →   Scaling factor: 1
#> ✔ Returning transformed image

ggplot(transf_res$xy_transf, aes(tr_x, tr_y)) +
  geom_point(color = "red", alpha = 0.5) +
  geom_segment(aes(x = 0, y = 0.5*19242, xend = 0.2*18107, yend = 0.5*19242),
               arrow = arrow(length = unit(0.5, "cm"))) +
  geom_vline(xintercept = 0.2*18107, linetype = "dashed") +
  geom_segment(aes(x = 0.5*18107, y = 19242, xend = 0.5*18107, yend = 0.8*19242),
               arrow = arrow(length = unit(0.5, "cm"))) +
  geom_hline(yintercept = 0.8*19242, linetype = "dashed") +
  scale_x_continuous(limits = c(0, 18107), expand = c(0, 0)) +
  scale_y_reverse(limits = c(19242, 0), expand = c(0, 0)) +
  labs(x = expression("x"["transformed"]),
       y = expression("y"["transformed"]),
       title = "20% right, 20% up, 30 deg rotation") +
  theme_void() +
  theme(axis.text = element_text(),
        axis.title.x = element_text(),
        axis.title.y = element_text(angle = 90)) +
  coord_fixed() +
  # Insert H&E image
  inset_element(p = as.raster(transf_res$im_transf),
                left = 0, bottom = 0,
                right = 1, top = 1,
                on_top = FALSE)
#> Warning: Removed 27 rows containing missing values (`geom_point()`).


library(semla)
library(dplyr)

se_mbrain <- readRDS(system.file("extdata/mousebrain", "se_mbrain", package = "semla"))
se_mcolon <- readRDS(system.file("extdata/mousecolon", "se_mcolon", package = "semla"))
se_merged <- MergeSTData(se_mbrain, se_mcolon) |>
  LoadImages()
#> 
#> ── Loading H&E images ──
#> 
#> ℹ Loading image from /private/var/folders/91/twz8ld_x3f98sr9yc2hq9xpn47blx2/T/RtmpQDm3p7/temp_libpathed1b712617f8/semla/extdata/mousebrain/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 600x565 to 400x377 pixels
#> ℹ Loading image from /private/var/folders/91/twz8ld_x3f98sr9yc2hq9xpn47blx2/T/RtmpQDm3p7/temp_libpathed1b712617f8/semla/extdata/mousecolon/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 541x600 to 400x444 pixels
#> ℹ Saving loaded H&E images as 'rasters' in Seurat object

# Define rigid transformations for section 2
transforms <- generate_rigid_transform(sampleID = 2, angle = 30, mirror_x = TRUE)

# Apply transformations
se_merged <- RigidTransformImages(se_merged, transforms = transforms)
#> 
#> ── Transforming images ──
#> 
#> ℹ Found transformations for sample(s): 2
#> ℹ Transforming image 2
#> ℹ Fetched spot coordinates
#> ℹ Supplied transformations are valid
#> →   Mirror along x-axis: TRUE
#> →   Mirror along y-axis: FALSE
#> →   Rotation angle: 30
#> →   Translation along x axis: 0%
#> →   Translation along y axis: 0%
#> →   Scaling factor: 1
#> ✔ Returning transformed image
#> ℹ Image transformation complete.

# Plot transformed image
MapFeatures(se_merged, features = "Th", image_use = "transformed")


# Define rigid tranformations for all sections
transforms <- bind_rows(generate_rigid_transform(sampleID = 1, angle = 30, mirror_x = TRUE),
                        generate_rigid_transform(sampleID = 2, angle = 60))
# Apply transformations
se_merged <- RigidTransformImages(se_merged, transforms = transforms)
#> 
#> ── Transforming images ──
#> 
#> ℹ Found transformations for sample(s): 1, 2
#> ℹ Transforming image 1
#> ℹ Fetched spot coordinates
#> ℹ Supplied transformations are valid
#> →   Mirror along x-axis: TRUE
#> →   Mirror along y-axis: FALSE
#> →   Rotation angle: 30
#> →   Translation along x axis: 0%
#> →   Translation along y axis: 0%
#> →   Scaling factor: 1
#> ✔ Returning transformed image
#> ℹ Transforming image 2
#> ℹ Fetched spot coordinates
#> ℹ Supplied transformations are valid
#> →   Mirror along x-axis: FALSE
#> →   Mirror along y-axis: FALSE
#> →   Rotation angle: 60
#> →   Translation along x axis: 0%
#> →   Translation along y axis: 0%
#> →   Scaling factor: 1
#> ✔ Returning transformed image
#> ℹ Image transformation complete.

# Plot transformed image
MapFeatures(se_merged, features = "Th", image_use = "transformed")