https://github.com/QBioLab/CountmRNA.jl
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Tip revision: 27fa41066bf09a3c1ca00fd333f72755e481b16f authored by H.F on 13 April 2021, 10:57 UTC
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Tip revision: 27fa410
splitcell.jl
using FileIO
using Images
using ImageSegmentation
using Statistics

"""
Use Laplace of Gaussian(LoG) filter extract cell from raw 3d image
Version Comment
0.1		initial 
0.2		only LoG
"""

"""
Generate border form watershed result
"""
function watershedborder(watershed_segments)
    marker_border = BitArray(undef, size(watershed_segments.image_indexmap));
    marker_border .= false
    for label in watershed_segments.segment_labels
        marker_border .|= ((watershed_segments.image_indexmap.==label) .⊻ erode(watershed_segments.image_indexmap .==label));
    end
    marker_border;
end

"""
Use LoG fiter raw image to extract cell
"""
function split_cell_LoG(stack::Array{Gray{Normed{UInt16,16}},4}; 
                        LoG::Integer=40, thres = -1e-7)
	println("Applying LoG(40) at Maximum Z Projection")
    #img_edge = zeros(N0f16, 1900, 1300, time);
    #mask_edge = zeros(Int16, 1900, 1300, time);
    h, w, d, time = size(stack)
    #local mask_markers = zeros(Bool, h, w, time);
    local mask_markers = Array{Bool}(undef, h, w, time);
	GC.gc() # garbage clean imediately to avoid double free insize threads.@threads
    #@inbounds Threads.@threads for t in 1:time  #use 40 threads slow down speed. may due to gc time
    @inbounds for t in 1:time  #use 40 threads slow down speed. may due to gc time
		# remove possion noise with median filter on maximum z-project image
		#local imgx = mapwindow(median!, 
        # maximum(view(stack, :, :, :, t), dims=3)[:,:,1], (5,5));
        # LoG will blur image to low image struture under \sigma,
        # So I remove median filter
        local imgx = maximum(view(stack, :, :, :, t), dims=3)[:,:,1];
		# extract intensity info with LoG
        mask_markers[:,:,t] = imfilter(imgx, Kernel.LoG(LoG)) .< thres ;
        #imgx_dist = distance_transform(feature_transform(imgx_log));
		# filter markers for watershed
        #imgx_markers = label_components( imgx_dist .> 50);
		#mask_markers[:,:,i] = imgx_markers
        #imgx_segments = watershed( imfilter(1 .- imgx, Kernel.gaussian(9)), imgx_markers);
        #img_edge[:,:,i] = .~watershedborder(imgx_segments).*imgx;
        #mask_clear[:,:,i] = extract_nucleus( imgx, imgx_segments) .> 0;
		#mask_edge[:,:,i] = imgx_segments.image_indexmap;
        #print("*");
    end
	println("Done")
    mask_markers;
end

#data_dir = "/datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF";
#img_16_2 = load(File(format"TIFF", "$data_dir/20200316/HE7-11-1-80uw-PWM_1_s2.ome.tiff"));

#@time edge, clear = split_cell_LoG(img_16_2, 137);
#res_dir = "/datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl"
#save("output/img_16_2_edge_all.tiff", edge);
#save("output/img_16_2_clear_all.tiff", clear);
#h5write("output/img_16_2_clear_all.h5", "img", rawview(clear));
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