Revision a07533c9ea81777f61634566429ee801da8231da authored by hf on 12 May 2020, 13:56:04 UTC, committed by hf on 12 May 2020, 13:56:04 UTC
1 parent 7981563
test15.jl
include("splitcell.jl")
include("lineage.jl");
include("segmentation3d.jl")
include("normalization3d.jl")
include("tiffxml.jl");
include("julia2ims.jl")
#
const data_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200315";
const ret_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200315_result/output";
#for s in 3:19
#function playing(s::Int)
#
#cell = zeros(Gray{Normed{UInt16,16}}, 512, 512, *20)
#for in 19:20
#for s in 19
function playing(s)
println("Loading $s")
@time img = load(File(format"TIFF","$data_dir/HE7-11-1-80uw-const_1_s$s.ome.btf.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);
@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);
#cell = zeros(Gray{Normed{UInt16,16}}, 512, 512, t_len*20)
for index in 1:length(longlived_labels)
println("tracking cell $index")
@time cell = pick_cell(img, longlived_maps, longlived_labels[index], tracks[:,:,index],
livingtime[index]);
@time cell_nu, cell_th = extract3dnucleus(cell);
@time cell_nu_nor, nor_para = normalize(cell_nu);
save("$ret_dir/d15s$(s)-$index.jld", "threshold", cell_th, "normal", nor_para,
"livingtime", livingtime[index])
save2ims( reinterpret.(reshape(cell_nu_nor,(512,512,20,t_len))),
"$ret_dir/d15s$(s)-$index.ims")
#GC.gc()
end
nothing
end
for img_index in parse(Int, ARGS[1]):parse(Int, ARGS[2])
@time playing(img_index)
end
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