Very often the fov_position coordinates are unaligned with the cell centroids.
It could be helpful a function to move the fov positions by adding/subtracting x/y coordinates from the loaded fov positions.
A starting code point for this could be
fovpos_file <- list.files(cospath, "fov_positions_file.csv", full.names=TRUE)
fov_positions <- as.data.frame(data.table::fread(fovpos_file, header=TRUE))
f1 <- fov_positions[fov_positions$FOV %in%fovs,]
x_shift_px <- y_shift_px <- 80
fov_px <- 4239.291
f1 <- f1 |>
dplyr::mutate(
x_global_px = x_global_mm / 0.12028 * 1000 + x_shift_px,
y_global_px = y_global_mm / 0.12028 * 1000 - fov_px + y_shift_px
)
Very often the fov_position coordinates are unaligned with the cell centroids.
It could be helpful a function to move the fov positions by adding/subtracting x/y coordinates from the loaded fov positions.
A starting code point for this could be