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
tiff2ims1215_2.jl
using FileIO
using Printf
include("julia2ims.jl")
"""
20201216: Package Spinning disk tif stack to imaris
"""
src_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_again/20201215/sCMOS"
out_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_again/20201215"
#src_dir = ARGS[1]
t_len = 30 # 29-58 time point,
z_len = 20
pos_len = 40
buffer = zeros(N0f16, 1900, 1300, z_len*t_len*pos_len)
img_num = 866
raw = load(File(format"TIFF", "$src_dir/HE7-1NLS-uw-PWM_1_MMStack_25.ome.tif"))
buffer[:, :, 1:116] = raw[:, :, 751:end] # push 116 slice
Threads.@threads for index in 26:52 # 27 file here, remain 618 slice
println(index)
filename = "HE7-1NLS-uw-PWM_1_MMStack_$index.ome.tif"
raw = load(File(format"TIFF", "$src_dir/$filename"))
id = (index-26)*img_num + 1 + 116
buffer[:, :, id:id+img_num-1] = raw
GC.gc()
end
GC.gc()
raw = load(File(format"TIFF", "$src_dir/HE7-1NLS-uw-PWM_1_MMStack_53.ome.tif"))
buffer[:, :, end-502+1:end] = raw[:, :, 1:502] # push 502 slice
buffer = reshape(buffer, (1900, 1300, z_len, t_len*pos_len))
Threads.@threads for pos in 1:pos_len
imsname = @sprintf("%s/pos%02d-2.tiff", out_dir, pos)
#save2ims(reinterpret(UInt16, buffer[:, :, :, :, pos]),
# imsname, dx=0.108, compression=1)
save(imsname, reshape(buffer[:, :, :, pos:40:end],
(1900, 1300, z_len*t_len)))
end