3D-rendering

Adult zebrafish 3D rendering

install.packages("imager") install.packages("rgl")

library(imager) library(rgl)

Function to load a z-stack from a folder

load_zstack <- function(folder) { file_list <- list.files(folder, pattern = "\.tif$", full.names = TRUE) zstack <- lapply(file_list, load.image) zstack <- simplify2array(zstack) # Convert list to array return(zstack) }

Load z-stacks from different folders

folder1 <- "/path/to/folder1" folder2 <- "/path/to/folder2"

zstack1 <- load_zstack(folder1) zstack2 <- load_zstack(folder2)

Assuming zstack1 and zstack2 have the same x and y dimensions

combined_zstack <- abind::abind(zstack1, zstack2, along = 3) # Combine along the z-axis

Install abind if not already installed

install.packages("abind")

Open a 3D plot

open3d()

Create a 3D surface for each slice in the z-stack

for (i in 1:dim(combined_zstack)[3]) { slice <- combined_zstack[,,i] surface3d(1:dim(slice)[1], 1:dim(slice)[2], matrix(i, nrow = dim(slice)[1], ncol = dim(slice)[2]), col = gray(slice/max(slice)), add = TRUE) }

Optionally adjust the viewpoint

rgl.viewpoint(theta = 30, phi = 30, zoom = 0.8)

Optionally add axes, labels, etc.

decorate3d()

To interact with the plot, use rglwidget() to embed it in a Shiny app or an R Markdown document

For static plots, use rgl.snapshot() to export as an image

Export as an image

rgl.snapshot("3d_figure.png")

For interactive visualization in R Markdown

library(htmlwidgets) saveWidget(rglwidget(), "3d_figure.html")