Raw File
{
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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "Collapsed": "false"
   },
   "outputs": [],
   "source": [
    "using FileIO\n",
    "using Plots\n",
    "using Images\n",
    "using ImageSegmentation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 465,
   "metadata": {
    "Collapsed": "false"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "export_cell (generic function with 1 method)"
      ]
     },
     "execution_count": 465,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "function find_nearest(root, next_level, maxdistance)\n",
    "    nucleus_distance = [sum(abs.(root .- next_level[i])) for i in 1:length(next_level)]\n",
    "    mindist, mindist_index = findmin(nucleus_distance);\n",
    "    if mindist < maxdistance\n",
    "        return mindist_index\n",
    "    else\n",
    "        return nothing\n",
    "    end\n",
    "end\n",
    "\n",
    "function buildtree(root::Int, position)\n",
    "    tree = []\n",
    "    height = length(position)\n",
    "    level = 2\n",
    "    child = find_nearest(position[1][root], position[level], 100);\n",
    "    while( child ≠ nothing && level<height)\n",
    "        push!(tree, child)\n",
    "        child = find_nearest(position[level][child], position[level+=1], 100)\n",
    "        #print(\"$level \")\n",
    "    end\n",
    "    tree\n",
    "end\n",
    "\n",
    "function generate_path(pos_map)\n",
    "    all_path = []\n",
    "    for root in 1:length(pos_map[1])\n",
    "        tree = buildtree(root, pos_map);\n",
    "        if length(tree) > 70\n",
    "            path = [pos_map[i+1][tree[i]] for i in 1:length(tree) ];\n",
    "            push!(all_path, path)\n",
    "        end\n",
    "    end\n",
    "    all_path;\n",
    "end\n",
    "\n",
    "function export_cell(track, imgs)\n",
    "    height, width = size(imgs[:,:,1]);\n",
    "    #Acrop_img = zeros(height, width, length(track));\n",
    "    crop_img = zeros(700, 700, length(track)*20);\n",
    "    for t in 1:length(track)\n",
    "        x, y = Int.(floor.(track[t]));\n",
    "        xmin, xmax, ymin, ymax = x-349 , x+350,  y-349, y+350\n",
    "        if xmin < 1\n",
    "            xmax = xmax - xmin + 1\n",
    "            xmin = 1\n",
    "        end\n",
    "        if xmax > 1900\n",
    "            xmin = xmin - (xmax-1900)\n",
    "            xmax = 1900\n",
    "        end\n",
    "        if ymin < 1\n",
    "            ymax = ymax - ymin +1\n",
    "            ymin = 1\n",
    "        end\n",
    "        if ymax > 1300\n",
    "            ymin = ymin - (ymax-1300)\n",
    "            ymax = 1300\n",
    "        end\n",
    "        masked_cell= (data[\"edge\"][:,:,t] .== data[\"edge\"][x, y, t] )\n",
    "        for i in 1:20\n",
    "            crop_img[:,:,20*(t-1)+i] =(masked_cell.*raw[:,:,20*(t-1)+i])[xmin:xmax, ymin:ymax]\n",
    "        end\n",
    "    end\n",
    "    crop_img;\n",
    "end"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "raw = load(File(format\"TIFF\", \"../mRNA_confocal_hamamatsu-60X-TIRF/20200316/HE7-11-1-80uw-PWM_1_s2.ome.tiff\"));"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 356,
   "metadata": {
    "Collapsed": "false"
   },
   "outputs": [],
   "source": [
    "data = load(\"mask4stat.jld\");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 357,
   "metadata": {
    "Collapsed": "false"
   },
   "outputs": [],
   "source": [
    "nucleus_pos = [ component_centroids(label_components(data[\"nucleus\"][:,:,i])) for i in 1:size(data[\"nucleus\"])[3] ];"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 374,
   "metadata": {},
   "outputs": [],
   "source": [
    "cells = generate_path(nucleus_pos);"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 380,
   "metadata": {},
   "outputs": [
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      ]
     },
     "execution_count": 380,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "plot( xlim=(0,1900), ylim=(0,1900))\n",
    "map(i->scatter!(i), cells);\n",
    "plot!()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 466,
   "metadata": {},
   "outputs": [],
   "source": [
    "for i in 1: length(cells)\n",
    "    save(\"path$i.tiff\", N0f16.(export_cell(cells[i], raw)))\n",
    "end"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 393,
   "metadata": {},
   "outputs": [],
   "source": [
    "img_export = N0f16.(export_cell(cells[1], raw));"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 439,
   "metadata": {},
   "outputs": [],
   "source": [
    "test = img_export[:,:,1] .> 0;\n",
    "minx = miny = 0;\n",
    "maxx = maxy = 0;\n",
    "\n",
    "for y in 1: size(test)[2]\n",
    "    if (miny==0) && (sum(test[:, y])>0)\n",
    "        miny = y;\n",
    "    end\n",
    "    if (miny > 0) && (sum(test[:, y])==0)\n",
    "        maxy = y-1;\n",
    "        break\n",
    "    end\n",
    "end\n",
    "\n",
    "for x in 1: size(test)[1]\n",
    "    if (minx==0) && (sum(test[x, :])>0)\n",
    "        minx = x;\n",
    "    end\n",
    "    if (minx > 0) && (sum(test[x, :])==0)\n",
    "        maxx = x-1;\n",
    "        break\n",
    "    end\n",
    "end"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 447,
   "metadata": {},
   "outputs": [],
   "source": [
    "save(\"path1_roi.tiff\", N0f16.(export_cell(cells[1], raw))[minx:maxx, miny:maxy, :])"
   ]
  }
 ],
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  "kernelspec": {
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  "language_info": {
   "file_extension": ".jl",
   "mimetype": "application/julia",
   "name": "julia",
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 "nbformat": 4,
 "nbformat_minor": 4
}
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