include("splitcell.jl")
include("lineage.jl");
include("segmentation3d.jl")
include("normalization3d.jl")
include("julia2ims.jl")
data_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF";
ret_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200319_result/output";
#for s in 3:19
#for s in 2:20
function playing(s)
println("Loading $s")
@time img = load(File(format"TIFF","$data_dir/20200319/HE7-1NLS-22uw-const_1_s$s.ome.tiff"));
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);
for index in 1:length(longlived_labels)
println("tracking cell $index")
@time local cell = pick_cell(img, longlived_maps, longlived_labels[index], tracks[:,:,index],
livingtime[index]);
@time cell_nu, cell_th = extract3dnucleus(cell);
@time cell_nu_nor, nor_para = normalize(cell_nu);
save("$ret_dir/d19s$(s)-$index.jld", "threshold", cell_th, "normal", nor_para,
"livingtime", livingtime[index], "track", tracks[:,:,index])
save2ims(reinterpret.(reshape(cell_nu_nor, (512,512,20,t_len))),
"$ret_dir/d19s$(s)-$index.ims")
end
GC.gc()
end
for i in parse(Int, ARGS[1]):parse(Int, ARGS[2])
playing(i)
end