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
test22.jl
include("splitcell.jl")
include("lineage.jl");
include("segmentation3d.jl")
include("normalization3d.jl")
include("julia2ims.jl")
using HDF5
using Images
using Dates
data_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322";
ret_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322_result/output";
#for s in 3:19
#for s in 2:20
function playing(s)
println("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
println("$(Dates.now()) Loading $s")
#@time img = load(File(format"TIFF","$data_dir/HE7-11-1-80uw-const_3_s$s.ome.tiff"));
@time img = loadims("$data_dir/HE7-1NLS-85uw-PWM_1_s$s.ome.ims");
GC.gc()
println("Load done")
t_len = size(img)[3]รท20
@time markers = split_cell_LoG(img, t_len);
GC.gc()
@time time_line, longlived_labels, livingtime, time_line_whole =
find_time_line(markers);
if length(longlived_labels) == 0
println("No longlived cells found, skipping")
return nothing
end
@time split_contacted_cell!(time_line, longlived_labels, livingtime, time_line_whole);
tracks = walking(time_line, longlived_labels, livingtime);
@time longlived_maps, watershed_maps = grant_domain(img, time_line, longlived_labels, livingtime, time_line_whole);
#save("$ret_dir/d21s$(s)-watershed.jld", "maps", watershed_maps)
for index in 1:length(longlived_labels)
println("tracking cell $index")
@time local cell = pick_cell(img, longlived_maps, longlived_labels[index], tracks[:,:,index],
livingtime[index]);
@time cell_nu, nucleus_size, nucleus_th = extract3dnucleus(cell);
@time cell_nu_nor, nor_para = normalize(cell_nu);
save("$ret_dir/d22s$(s)-$index.jld", "threshold", nucleus_th, "normal", nor_para,
"livingtime", livingtime[index], "track", tracks[:,:,index], "size", nucleus_size)
save2ims(reinterpret.(reshape(cell_nu_nor, (512,512,20,t_len))),
"$ret_dir/d22s$(s)-$index.ims")
end
GC.gc()
end
println("Processing $data_dir, output $ret_dir")
for i in parse(Int, ARGS[1]):parse(Int, ARGS[2])
playing(i)
end