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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Tip revision: 27fa410
tiff2ims1215_1.jl
using TIFF
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"
t_len = 28 #1-28
z_len = 20
pos_len = 40
buffer = zeros(N0f16, 1900, 1300, z_len*t_len*pos_len)
img_num = 866
Threads.@threads for index in 0:24
println(index)
filename = "HE7-1NLS-uw-PWM_1_MMStack_$index.ome.tif"
raw = TIFF.load("$src_dir/$filename")
id = index*img_num + 1
buffer[:, :, id:id+img_num-1] = raw.data
GC.gc()
end
#Threads.@threads for index in 25:54
# filename = "HE7-1NLS-uw-PWM_1_MMStack_$index.ome.tif"
# raw = load(File(format"TIFF", "$src_dir/$filename"))
# id = index*img_num + 1
# buffer[:, :, id:id+img_num-1] = raw.data
# GC.gc()
#end
t0 = 25*866
remain = t_len*z_len*pos_len - t0 # 750
raw = load(File(format"TIFF", "$src_dir/HE7-1NLS-uw-PWM_1_MMStack_25.ome.tif"))
buffer[:, :, t0+1:end] = raw[:, :, 1:remain]
buffer = reshape(buffer, (1900, 1300, z_len, t_len*pos_len))
Threads.@threads for pos in 1:pos_len
imsname = @sprintf("%s/pos%02d-1.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