Spatial-biocomputation/process_code_Madrid.R at main · BiocomputationLab/Spatial-biocomputation · GitHub

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install.packages("devtools")
devtools::install_github("ajfedorec/plateR")
library(plateR)
install.packages("imager")
library(imager)

dir_path <- "C:/Users/Paula/Desktop/PhD/2025/Characterization OT-2/20260122_rep5"
output_path <- file.path(dir_path, "converted")


# List of images
files <- list.files(dir_path, pattern = "\\.png$", full.names = TRUE)

for (f in files) {
  img <- load.image(f)
  img <- mirror(img, "x")

  # Decides the channel accroding to the name of the document, in this case Alexa is green Colorimetric is red channel"
  if (grepl("Alexa", f, ignore.case = TRUE)) {
    img_use <- as.cimg(img[,,,3])  # blue
  } else if (grepl("Colorimetric", f, ignore.case = TRUE)) {
    img_use <- as.cimg(img[,,,1])  # red
  } else {
    img_use <- grayscale(img)
  }

  # Save with new name
  new_name <- file.path(output_path, paste0(basename(tools::file_path_sans_ext(f)), "_converted.png"))
  save.image(img_use, new_name)

  cat("Guardada:", new_name, "\n")
}

##### Second part of the code from Fedorec et al., 2024, plateR  #####

dir_path <- "C:/Users/Paula/Desktop/PhD/2025/Characterization OT-2/20260218-not+not/converted/20h-plate2"  # replace ... with img folder name (including /00000/)

plate_number = 2
replica = 1
t = 20

img_settings_list <- list(c(exposure=20000,
                            intensity=1,
                            panel="blue",
                            system="old",
                            plate_number = plate_number,
                            replica = replica,
                            t = t),
                          c(exposure=20000,
                            intensity=3,
                            panel="blue",
                            system="old",
                            plate_number = plate_number,
                            replica = replica,
                            t = t),
                          c(exposure=40000,
                            intensity=3,
                            panel="blue",
                            system="old",
                            plate_number = plate_number,
                            replica = replica,
                            t = t),
                          c(exposure=60000,
                            intensity=5,
                            panel="blue",
                            system="old",
                            plate_number = plate_number,
                            replica = replica,
                            t = t),
                          c(exposure=4000,
                            intensity=0.7,
                            panel="red",
                            system="old",
                            plate_number = plate_number,
                            replica = replica,
                            t = t))


## change these settings as you need.
plateR::process_img_dir(dir_path = dir_path,
                img_settings_list = img_settings_list,
                align_filename = '0004.png',
                invert = F,
                rotate = F,
                experiment_type = 'colony',
                normalise = F,
                stencil_proportion = 0.5,
                proportion_centered = T,
                plate_type = '6-well',
                num_wells = 384,
                px_per_mm = 12.5, # if you already know the image alignment you don't have to go through the alignment process again
                tl_corner = NA,
                deg_rotation = NA,
                well_ratio = 0.95,
                in_parallel = TRUE, # process images in parallel, should speed up the process
                blur = 3)