Revision 27fa41066bf09a3c1ca00fd333f72755e481b16f authored by H.F on 13 April 2021, 10:57:05 UTC, committed by H.F on 13 April 2021, 10:57:05 UTC
1 parent f3455fe
Raw File
tiff2ims1215_3.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 = 20 # 59- 78time 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_53.ome.tif"))
buffer[:, :, 1:364] = raw[:, :, 503:end] # push 364 slice

Threads.@threads for index in 54:71 # 18 file here, remain 412 slice
    println(index)
    filename = "HE7-1NLS-uw-PWM_1_MMStack_$index.ome.tif"
    raw = load(File(format"TIFF", "$src_dir/$filename"))
    id = (index-54)*img_num + 1 + 364
    buffer[:, :, id:id+img_num-1] = raw
    GC.gc()
end

raw = load(File(format"TIFF", "$src_dir/HE7-1NLS-uw-PWM_1_MMStack_72.ome.tif"))
buffer[:, :, end-48+1:end] = raw[:, :, 1:48] # push 48 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-3.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
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