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thewtex/RichardsonLucyDeconvolution.ipynb

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Light sheet Richardson-Lucy deconvolution
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RichardsonLucyDeconvolution.ipynb
{
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{
"cell_type": "code",
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"source": [
"import os\n",
"\n",
"import dask.array as da\n",
"import itk\n",
"import numpy as np\n",
"\n",
"from itkwidgets import view"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"data_dir = '/home/kitware/data/LightSheet/m4/'"
]
},
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"source": [
"image = da.from_zarr(os.path.join(data_dir, 'stacked.zarr'))"
]
},
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"cell_type": "code",
"execution_count": 4,
"metadata": {},
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"cell_type": "code",
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"outputs": [
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"Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageUS3; proxy …"
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"source": [
"# Note: 488nm corresponds to the first channel of the image data\n",
"psf_file = os.path.join(data_dir, 'psfs_z0p1/PSF_488nm_dz100nm.tif')"
]
},
{
"cell_type": "code",
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"psf = itk.array_from_image(itk.imread(psf_file))\n",
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{
"cell_type": "code",
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"metadata": {},
"outputs": [
{
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"view(psf_sub, slicing_planes=True, shadow=False, ui_collapsed=True)"
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"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"def richardson_lucy_deconvolution(img, psf, iterations=1):\n",
" image = itk.image_view_from_array(np.ascontiguousarray(img))\n",
" kernel = itk.image_view_from_array(np.ascontiguousarray(psf))\n",
" \n",
" deconvolved = itk.richardson_lucy_deconvolution_image_filter(image,\n",
" kernel_image=kernel,\n",
" number_of_iterations=iterations)\n",
" return itk.array_from_image(deconvolved)\n",
"\n",
"deconvolved = richardson_lucy_deconvolution(image_chunk, psf_sub)"
]
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"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
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