{ "cells": [ { "cell_type": "markdown", "id": "27ef9ff2", "metadata": {}, "source": [ "# Morphology: Trees (Notebook)" ] }, { "cell_type": "markdown", "id": "6afd6e86", "metadata": {}, "source": [ "[](https://colab.research.google.com/github/Poirazi-Lab/DendroTweaks/blob/main/docs/source/tutorials/Morphology_trees.ipynb)" ] }, { "cell_type": "markdown", "id": "d51c8808", "metadata": {}, "source": [ "This tutorial will guide you through creating a neuronal morphology representation step by step. First, we will read data from an SWC file using the `SWCReader` class. Next, we will use factory functions to create a `PointTree` i.e. the graph-tree representation of our morphological reconstruction. Then, we will split the point tree into sections to obtain a `SectionTree`. Finally, we will build a `SegmentTree` that divides our cell into computational segments for simulation." ] }, { "cell_type": "markdown", "id": "0ebfae05", "metadata": {}, "source": [ "
load_morphology method of the Model class. Only follow the steps below if the method fails to read the morphology automatically or if you want to manually intervene in the process.\n",
"| \n", " | Index | \n", "Type | \n", "Domain | \n", "Color | \n", "X | \n", "Y | \n", "Z | \n", "R | \n", "Parent | \n", "
|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "1 | \n", "1 | \n", "soma | \n", "#E69F00 | \n", "11.621167 | \n", "104.434833 | \n", "-6.694167 | \n", "10.218962 | \n", "-1 | \n", "
| 1 | \n", "2 | \n", "1 | \n", "soma | \n", "#E69F00 | \n", "11.621167 | \n", "94.215871 | \n", "-6.694167 | \n", "10.218962 | \n", "1 | \n", "
| 2 | \n", "3 | \n", "1 | \n", "soma | \n", "#E69F00 | \n", "11.621167 | \n", "114.653796 | \n", "-6.694167 | \n", "10.218962 | \n", "1 | \n", "
| 3 | \n", "4 | \n", "2 | \n", "axon | \n", "#F0E442 | \n", "5.260000 | \n", "92.000000 | \n", "-9.100000 | \n", "0.295000 | \n", "1 | \n", "
| 4 | \n", "5 | \n", "2 | \n", "axon | \n", "#F0E442 | \n", "5.290000 | \n", "91.490000 | \n", "-9.100000 | \n", "0.295000 | \n", "4 | \n", "