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DOC: Simplify ITK LabelImages segmentation
Keep it the same as the scikit-image segmentation for clarity.
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‎examples/LabelImages.ipynb‎

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"# Install dependencies for this example\n",
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"# Note: This does not include itkwidgets, itself\n",
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"import sys\n",
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"!{sys.executable} -m pip install -U itk itk-totalvariation scikit-image"
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"!{sys.executable} -m pip install -U itk scikit-image"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "436f06a0454f4e0abee8cbf15573015e",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(annotations=False, cmap=['BrBG'], geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"image = itk.imread(file_name, itk.F)\n",
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"image = itk.imread(file_name)\n",
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"\n",
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"view(image, cmap=itkwidgets.cm.BrBG, annotations=False, vmax=800, ui_collapsed=True)"
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]
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"outputs": [],
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"source": [
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"# Segment the cells\n",
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"smoothed = itk.prox_tv_image_filter(image, weights=50, maximum_number_of_iterations=3)\n",
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"smoothed = itk.smoothing_recursive_gaussian_image_filter(image)\n",
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"\n",
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"LabelMapType = itk.Image[itk.UC, 3]\n",
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"thresholded = itk.moments_threshold_image_filter(smoothed,\n",
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" inside_value=0,\n",
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" outside_value=1)\n",
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"\n",
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"threshold_filter = itk.MomentsThresholdImageFilter[type(smoothed), LabelMapType].New(smoothed)\n",
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"threshold_filter.SetInsideValue(0)\n",
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"threshold_filter.SetOutsideValue(1)\n",
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"threshold_filter.Update()\n",
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"threshold = threshold_filter.GetThreshold()\n",
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"thresholded = threshold_filter.GetOutput()"
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"connected_components = itk.connected_component_image_filter(thresholded)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 19,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "69dfe9c8df3d41a889e9c7b63f114284",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.22, interpolation=False, point_sets=[], rendered_label_image=<itk.itkIm…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"view(label_image=thresholded)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 20,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "33c0cb1ad92241a49728735b67d1f83f",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.22, interpolation=False, point_sets=[], rendered_label_image=<itk.itkIm…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"connected_components = itk.connected_component_image_filter(thresholded)\n",
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"\n",
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"view(label_image=connected_components)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 22,
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"execution_count": null,
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"metadata": {
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"scrolled": true
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},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "94c8055aff1a4cb89923c78072fa305b",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.5, interpolation=False, label_image_names=[(0, 'Background'), (1, 'Firs…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"# We can combine the label map with the intensity image, add names for the labels, etc.\n",
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"names = [(0, 'Background'), (1, 'First cell'), (2, 'Second cell')]\n",
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},
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{
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"cell_type": "code",
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"execution_count": 27,
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"execution_count": null,
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"metadata": {},
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"source": [
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "8327687db5c64422a16af110bb597b76",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(annotations=False, cmap=['BrBG'], geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"image = skimage.io.imread(file_name)\n",
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"\n",
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"metadata": {},
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"source": [
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "cdc8480801bc4792b2053812febdf00f",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.22, interpolation=False, point_sets=[], rendered_label_image=<itk.itk…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"view(label_image=connected_components)"
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]

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