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add new examples
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@Henley13
Henley13 committed May 5, 2020
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66 changes: 34 additions & 32 deletions examples/1 - Read and write images.ipynb
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{
"data": {
"text/plain": [
"['experience_1_dapi_fov_1.tif', 'experience_1_smfish_fov_1.tif', '.gitignore']"
"['.DS_Store',\n",
" 'experience_1_dapi_fov_1.tif',\n",
" 'experience_1_smfish_fov_1.tif',\n",
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"output_type": "stream",
"text": [
"Image 0\n",
"\r",
" shape: (1, 2, 23, 650, 500)\n",
"\r",
" dtype: uint16\n",
"Image 1\n",
"\r",
" shape: (1, 2, 23, 650, 500)\n",
"\r",
" dtype: uint16\n"
]
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"- for *.png*, *.jpg*, *.jpeg*, *.tif* or *.tiff* extensions use `bigfish.stack.read_image`\n",
"- for *.dv* extension use `bigfish.stack.read_dv`\n",
"- for *.npy* extension use `bigfish.stack.read_array`\n",
"- for *.npz* extension use `bigfish.stack.read_compressed`"
"- for *.npz* extension use `bigfish.stack.read_compressed`\n",
"- for *.csv* extension use `bigfish.stack.read_array_from_csv`"
]
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"source": [
"Same logic if you want to save images or arrays:\n",
"- for *.png*, *.jpg*, *.jpeg*, *.tif* or *.tiff* extensions use `bigfish.stack.save_image`\n",
"- for *.npy* extension use `bigfish.stack.save_array`"
"- for *.npy* extension use `bigfish.stack.save_array`\n",
"- for *.csv* extension use `bigfish.stack.save_array_to_csv`"
]
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{
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63 changes: 28 additions & 35 deletions examples/2 - Normalize and filter images.ipynb
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"titles = [\"LoG filter\", \"remove gaussian background\", \"remove mean background\"]\n",
"plot.plot_images(tensors, rescale=True, titles=titles, framesize=(13, 6), remove_frame=True)"
]
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