https://github.com/QBioLab/CountmRNA.jl
Tip revision: 27fa41066bf09a3c1ca00fd333f72755e481b16f authored by H.F on 13 April 2021, 10:57:05 UTC
upload running script
upload running script
Tip revision: 27fa410
visualization2_0315.jl
using FileIO
include("julia2ims.jl")
field = ["s1-1" "s4-3" "s4-6" "s5-6" "s9-5" "s9-4" "s10-2" "s11-4" "s12-1" "s13-3" "s13-1" "s14-1" "s14-6" "s14-4" "s14-8" "s16-5" "s16-1" "s21-1" "s22-8" "s23-1" "s27-5" "s34-3" ]
data_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200315";
output_dir = "$(data_dir)_visualization"
try
mkdir("$output_dir")
catch
end
function max_projection(cell)
println("Processing $cell")
#raw_img = load(File(format"TIFF", "$data_dir/HE7-11-1-80uw-const_3_$pos.ome.tiff"));
raw_img = loadims2("$(data_dir)_result/output/d15$cell.ims");
img_size = size(raw_img);
img_max = zeros(N0f16, img_size[1], img_size[2], Int(img_size[3]/20));
for i in 1:Int(img_size[3]/20)
img_max[:, :, i] = maximum(raw_img[:, :, (i-1)*20+1:i*20], dims=3);
end
save("$output_dir/$cell.tiff", img_max);
end
for cell in field
max_projection(cell)
end