https://github.com/QBioLab/CountmRNA.jl
Tip revision: 27fa41066bf09a3c1ca00fd333f72755e481b16f authored by H.F on 13 April 2021, 10:57:05 UTC
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upload running script
Tip revision: 27fa410
test0305.jl
include("splitcell.jl")
include("lineage.jl");
include("segmentation3d.jl")
include("normalization3d.jl")
include("julia2ims.jl")
using Printf
using Images
using Dates
data_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_IV/20210305";
ret_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_IV/20210305_result";
day = "05"
function playing(s)
println("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
println("$(Dates.now()) Loading $s")
local id = @sprintf("%02d", s)
@time img = Gray.(reinterpret(N0f16, loadims("$data_dir/pos$id.ims")));
#p_img = img .- df
GC.gc()
println("Load done")
t_len = size(img)[4]
@time markers = split_cell_LoG(img, LoG=40, thres=-1e-7);
GC.gc()
@time time_line, longlived_labels, livingtime, time_line_whole =
find_time_line(markers, shortest=80);
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 $index")
@time local cell = pick_cell(img , longlived_maps, longlived_labels[index],
tracks[:,:,index], livingtime[index]);
#TiffImages.save("$ret_dir/d$(day)s$id-$index_id.tiff", cell)
@time cell_nu, nucleus_size, nucleus_th = extract3dnucleus(cell);
local index_id = @sprintf("%02d", index)
@time cell_nu_nor, nor_para = normalize(cell_nu);
save("$ret_dir/d$(day)s$(id)-$index_id.jld", "threshold", nucleus_th, "normal", nor_para,
"livingtime", livingtime[index], "track", tracks[:,:,index], "size", nucleus_size)
save2ims(reinterpret.(cell_nu_nor), "$ret_dir/d$(day)s$id-$index_id.ims", compression=2)
end
GC.gc()
end
println("Processing $data_dir, output $ret_dir")
for i in parse(Int, ARGS[1]):parse(Int, ARGS[2])
#for i in parse(Int, ARGS[1]):4:parse(Int, ARGS[2])
playing(i)
end