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Merge pull request #62 from haesleinhuepf/git-bob-mod-RQLEp8C0YZ
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Enhanced documentation clarity in `quantitative_neighbor_maps.ipynb` by updating markdown cells.
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haesleinhuepf authored Aug 8, 2024
2 parents 0520676 + f39e3e7 commit 1087fca
Showing 1 changed file with 9 additions and 6 deletions.
15 changes: 9 additions & 6 deletions docs/60_data_visualization/quantitative_neighbor_maps.ipynb
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"cell_type": "markdown",
"metadata": {},
"source": [
"# Quantitative maps from neighbor statistics"
"# Quantitative maps from neighbor statistics\n",
"This notebook illustrates how to generate quantitative maps based on neighbor statistics using image processing libraries."
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"The example imge \"maize_clsm.tif\" was taken from the repository [mathematical_morphology_with_MorphoLibJ](https://github.com/dlegland/mathematical_morphology_with_MorphoLibJ) and is licensed by David Legland under [CC-BY 4.0 license](\n",
"https://github.com/dlegland/mathematical_morphology_with_MorphoLibJ/blob/master/LICENSE)"
"The example image \"maize_clsm.tif\" was taken from the repository [mathematical_morphology_with_MorphoLibJ](https://github.com/dlegland/mathematical_morphology_with_MorphoLibJ) and is licensed by David Legland under [CC-BY 4.0 license](https://github.com/dlegland/mathematical_morphology_with_MorphoLibJ/blob/master/LICENSE)."
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"# Starting point: Label map"
"# Starting point: Label map\n",
"First, we perform a segmentation process to obtain a labeled map of the cells using thresholding and Voronoi labeling."
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"## Nearest neighbor distance maps"
"## Nearest neighbor distance maps\n",
"We then compute maps of the average distance to the nearest neighbors for each labeled cell."
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"## Touching neighbor distance map"
"## Touching neighbor distance map\n",
"Finally, we create a map that shows the average distance to touching neighbors for each cell."
]
},
{
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