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Update wording in SWC tutorial (#536)
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michaeldeistler authored Dec 2, 2024
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4 changes: 2 additions & 2 deletions docs/tutorials/08_importing_morphologies.ipynb
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"cell_type": "markdown",
"metadata": {},
"source": [
"To work with `.swc` files, `Jaxley` implements a custom `.swc` reader. The reader traces the morphology and identifies all uninterrupted sections. These are then partitioned into branches, each of which will be approximated by a number of equally many compartments that can be simulated fully in parallel.\n",
"To work with `.swc` files, `Jaxley` implements a custom `.swc` reader. The reader traces the morphology and identifies all uninterrupted sections. These uninterrupted sections are called `branches` in `Jaxley`. Each `branch` is then further partitioned into `compartments`.\n",
"\n",
"To demonstrate this, let's import an example morphology of a Layer 5 pyramidal cell and visualize it."
]
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"source": [
"# import swc file into jx.Cell object\n",
"fname = \"data/morph.swc\"\n",
"cell = jx.read_swc(fname, ncomp=8) # Use four compartments per branch.\n",
"cell = jx.read_swc(fname, ncomp=8) # Use eight compartments per branch.\n",
"\n",
"# print shape (num_branches, num_comps)\n",
"print(cell.shape)\n",
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