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@anna-grim
anna-grim authored Jan 9, 2025
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14 changes: 7 additions & 7 deletions tutorials/1-soma_proposal_generation.ipynb
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" Soma Proposal Generation Algorithm\n",
" 1. Generate Initial Proposals - detect_blobs()\n",
" a. Smooth image with Gaussian filter to reduce false positives.\n",
" b. Laplacian of Gaussian (LoG) to enhance regions where the\n",
" intensity changes dramatically (i.e. higher gradient), then\n",
" apply a non-linear maximum filter.\n",
" b. Laplacian of Gaussian (LoG) to enhance regions where the gradient\n",
" changes rapidly, then apply a non-linear maximum filter.\n",
" c. Generate initial set of proposals by detecting local maximas\n",
" that lie outside of the image margins.\n",
" d. Shift each proposal to the brightest voxel in its neighborhood.\n",
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"\n",
"# Proposals: 1\n",
"# Rejects: 0\n",
"Runtime: 0.2150118350982666\n"
"Runtime: 0.21765899658203125\n"
]
},
{
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"proposals = spg.brightness_filtering(img_patch, proposals, 10)\n",
"proposals, rejects = gaussian_fitness_filtering(img_patch, proposals)\n",
"\n",
"# Report Results\n",
"print(\"\\n# Proposals:\", len(proposals))\n",
"print(\"# Rejects:\", len(rejects))\n",
"print(\"Runtime:\", time() - t0)\n",
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"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 100/100 [00:07<00:00, 3.70it/s]"
"100%|██████████| 100/100 [00:05<00:00, 15.45it/s]"
]
},
{
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"text": [
"\n",
"# Proposals Generated: 11\n",
"Runtime: 7.499921083450317\n"
"Runtime: 5.63988184928894\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"101it [00:19, 3.70it/s] "
"101it [00:19, 15.45it/s] "
]
}
],
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39 changes: 39 additions & 0 deletions tutorials/exaspim_image_prefixes.json
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{
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}

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