{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Ball and stick 1: Basic cell" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This is the first part of a several page tutorial that will ultimately build a ring network of mutlicompartment neurons running on a parallel machine.\n", "\n", "Best software engineering practice is to carefully design both the model and code. A well-designed system is easier to debug, maintain, and extend.\n", "\n", "This tutorial will take a functional bottom-up approach, building key components and refactoring as needed for a better software design instead of describing a complex design and filling in the pieces.\n", "\n", "This part of the tutorial builds a two-compartment neuron consisting of a soma and dendrite. This representation is known as a ball-and-stick model. After building the cell, we will attach some instrumentation to it to simulate and monitor its dynamics." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Load NEURON" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We of course begin by loading NEURON's main submodule `n`." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:09.591517Z", "iopub.status.busy": "2025-08-18T03:35:09.590573Z", "iopub.status.idle": "2025-08-18T03:35:10.642161Z", "shell.execute_reply": "2025-08-18T03:35:10.641729Z" } }, "outputs": [], "source": [ "from neuron import n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "As good practice, we'll load some unit definitions:" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:10.645984Z", "iopub.status.busy": "2025-08-18T03:35:10.645767Z", "iopub.status.idle": "2025-08-18T03:35:10.682933Z", "shell.execute_reply": "2025-08-18T03:35:10.682432Z" } }, "outputs": [], "source": [ "from neuron.units import ms, mV, µm" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We'll load the standard run library to give us high-level simulation control functions (e.g. running a simulation for a given period of time):" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:10.689020Z", "iopub.status.busy": "2025-08-18T03:35:10.688692Z", "iopub.status.idle": "2025-08-18T03:35:10.736611Z", "shell.execute_reply": "2025-08-18T03:35:10.736175Z" } }, "outputs": [ { "data": { "text/plain": [ "1.0" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.load_file(\"stdrun.hoc\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If we're running in Jupyter, we should allow interactive graphics inline so that we can explore our PlotShapes interactively; skip this line if you're not using Jupyter (it'll cause a syntax error):" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:10.910666Z", "iopub.status.busy": "2025-08-18T03:35:10.906880Z", "iopub.status.idle": "2025-08-18T03:35:40.969840Z", "shell.execute_reply": "2025-08-18T03:35:40.969402Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Matplotlib is building the font cache; this may take a moment.\n" ] } ], "source": [ "%matplotlib notebook" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Defining the cell morphology" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Create the sections" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "A ball-and-stick cell by definition consists of two parts: the soma (ball) and a dendrite (stick). We could define two Sections at the top level as in the previous tutorial, but that wouldn't give us an easy way to create multiple cells. Instead, let's define a BallAndStick neuron class. The basic boilerplate for defining any class in Python looks like:" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:40.976971Z", "iopub.status.busy": "2025-08-18T03:35:40.976731Z", "iopub.status.idle": "2025-08-18T03:35:40.980936Z", "shell.execute_reply": "2025-08-18T03:35:40.980565Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self):\n", " \"\"\"anything that should be done every time one of these is created goes here\"\"\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In our case in particular, every time we say that there is a BallAndStick cell, we should create the soma and the dendrite sections:" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:40.987868Z", "iopub.status.busy": "2025-08-18T03:35:40.987714Z", "iopub.status.idle": "2025-08-18T03:35:40.992566Z", "shell.execute_reply": "2025-08-18T03:35:40.991138Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self):\n", " self.soma = n.Section(\"soma\", self)\n", " self.dend = n.Section(\"dend\", self)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Any variables that describe properties of the cell must get stored as attributes of self. This is why we write self.soma instead of soma. Temporary variables, on the other hand, need not be prefixed with self and will simply stop existing when the initialization function ends.\n", "\n", "You will also note that we have introduced a new keyword argument for Section, namely the cell attribute. This will always be set to self (i.e. the current cell) to allow each Section to know what cell it belongs to." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Recall that we can check the topology via:" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.000086Z", "iopub.status.busy": "2025-08-18T03:35:40.999717Z", "iopub.status.idle": "2025-08-18T03:35:41.006030Z", "shell.execute_reply": "2025-08-18T03:35:41.005665Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "\n" ] }, { "data": { "text/plain": [ "1.0" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.topology()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "No sections were displayed. Why?\n", "\n", "The explanation is that we haven't actually created any such cells yet; we've only defined a rule for them. Let's go ahead and create our first cell:" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.012874Z", "iopub.status.busy": "2025-08-18T03:35:41.012721Z", "iopub.status.idle": "2025-08-18T03:35:41.017521Z", "shell.execute_reply": "2025-08-18T03:35:41.017144Z" } }, "outputs": [], "source": [ "my_cell = BallAndStick()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We again check the topology and see that the sections have in fact been created:" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.019091Z", "iopub.status.busy": "2025-08-18T03:35:41.018936Z", "iopub.status.idle": "2025-08-18T03:35:41.025237Z", "shell.execute_reply": "2025-08-18T03:35:41.024919Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "|-| <__main__.BallAndStick object at 0x7b2441e3dd90>.soma(0-1)\n", "|-| <__main__.BallAndStick object at 0x7b2441e3dd90>.dend(0-1)\n", "\n" ] }, { "data": { "text/plain": [ "1.0" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.topology()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Clearly there is a soma and a dendrite, but the cell identifier before each is not very friendly.\n", "\n", "We can specify how the cell displays using the `__repr__` method:" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.026881Z", "iopub.status.busy": "2025-08-18T03:35:41.026740Z", "iopub.status.idle": "2025-08-18T03:35:41.033515Z", "shell.execute_reply": "2025-08-18T03:35:41.033136Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self):\n", " self.soma = n.Section(\"soma\", self)\n", " self.dend = n.Section(\"dend\", self)\n", "\n", " def __repr__(self):\n", " return \"BallAndStick\"" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.035598Z", "iopub.status.busy": "2025-08-18T03:35:41.034910Z", "iopub.status.idle": "2025-08-18T03:35:41.043626Z", "shell.execute_reply": "2025-08-18T03:35:41.043235Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "|-| <__main__.BallAndStick object at 0x7b2441e3dd90>.soma(0-1)\n", "|-| <__main__.BallAndStick object at 0x7b2441e3dd90>.dend(0-1)\n", "\n" ] }, { "data": { "text/plain": [ "1.0" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.topology()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Our sections display based on the rule they were created with, not the new rule, so we need to recreate the cell:" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.045402Z", "iopub.status.busy": "2025-08-18T03:35:41.045113Z", "iopub.status.idle": "2025-08-18T03:35:41.049657Z", "shell.execute_reply": "2025-08-18T03:35:41.049281Z" } }, "outputs": [], "source": [ "my_cell = BallAndStick()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now we see something friendlier:" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.052877Z", "iopub.status.busy": "2025-08-18T03:35:41.051039Z", "iopub.status.idle": "2025-08-18T03:35:41.058560Z", "shell.execute_reply": "2025-08-18T03:35:41.058179Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "|-| BallAndStick.soma(0-1)\n", "|-| BallAndStick.dend(0-1)\n", "\n" ] }, { "data": { "text/plain": [ "1.0" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.topology()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "There's a problem though; do you see it?\n", "\n", "Every cell using this rule would print out the same cell identifier. So if we create a second cell:" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.062505Z", "iopub.status.busy": "2025-08-18T03:35:41.060097Z", "iopub.status.idle": "2025-08-18T03:35:41.064349Z", "shell.execute_reply": "2025-08-18T03:35:41.063990Z" } }, "outputs": [], "source": [ "my_other_cell = BallAndStick()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "and look at the topology:" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.066524Z", "iopub.status.busy": "2025-08-18T03:35:41.065939Z", "iopub.status.idle": "2025-08-18T03:35:41.073907Z", "shell.execute_reply": "2025-08-18T03:35:41.073549Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "|-| BallAndStick.soma(0-1)\n", "|-| BallAndStick.dend(0-1)\n", "|-| BallAndStick.soma(0-1)\n", "|-| BallAndStick.dend(0-1)\n", "\n" ] }, { "data": { "text/plain": [ "1.0" ] }, "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.topology()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "There is no way to tell the two somas apart and see which goes with which cell. To fix this, we'll pass in an identifier gid when we create the cell and have `__repr__` incorporate that into the name:" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.075552Z", "iopub.status.busy": "2025-08-18T03:35:41.075191Z", "iopub.status.idle": "2025-08-18T03:35:41.081606Z", "shell.execute_reply": "2025-08-18T03:35:41.079867Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self, gid):\n", " self._gid = gid\n", " self.soma = n.Section(\"soma\", self)\n", " self.dend = n.Section(\"dend\", self)\n", "\n", " def __repr__(self):\n", " return \"BallAndStick[{}]\".format(self._gid)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Important: the cell name (returned by `__repr__`) will be read when the Section is created, so any and all data that function needs -- here the `gid` -- must be stored before creating any Section objects." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now let's create our two cells:" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.085498Z", "iopub.status.busy": "2025-08-18T03:35:41.083274Z", "iopub.status.idle": "2025-08-18T03:35:41.087438Z", "shell.execute_reply": "2025-08-18T03:35:41.087052Z" } }, "outputs": [], "source": [ "my_cell = BallAndStick(0)\n", "my_other_cell = BallAndStick(1)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now when we look at the topology, we can tell the Sections belonging to the two cells apart:" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.090693Z", "iopub.status.busy": "2025-08-18T03:35:41.090543Z", "iopub.status.idle": "2025-08-18T03:35:41.097033Z", "shell.execute_reply": "2025-08-18T03:35:41.096662Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "|-| BallAndStick[0].soma(0-1)\n", "|-| BallAndStick[0].dend(0-1)\n", "|-| BallAndStick[1].soma(0-1)\n", "|-| BallAndStick[1].dend(0-1)\n", "\n" ] }, { "data": { "text/plain": [ "1.0" ] }, "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.topology()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We can tell which sections are the soma and which are dendrites. We can see which go with cell 0 and which go with cell 1, but there is nothing indicating that the dendrite is connected to the soma. This is because we have not told NEURON about any such relationships, so let's do so:" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Connect the sections" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We attach `self.dend` to the `self.soma` using the `connect` method:" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.098701Z", "iopub.status.busy": "2025-08-18T03:35:41.098557Z", "iopub.status.idle": "2025-08-18T03:35:41.104617Z", "shell.execute_reply": "2025-08-18T03:35:41.102691Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self, gid):\n", " self._gid = gid\n", " self.soma = n.Section(\"soma\", self)\n", " self.dend = n.Section(\"dend\", self)\n", " self.dend.connect(self.soma)\n", "\n", " def __repr__(self):\n", " return \"BallAndStick[{}]\".format(self._gid)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "As before, we must recreate the cells now that we've changed the rule:" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.106723Z", "iopub.status.busy": "2025-08-18T03:35:41.106060Z", "iopub.status.idle": "2025-08-18T03:35:41.111502Z", "shell.execute_reply": "2025-08-18T03:35:41.111137Z" } }, "outputs": [], "source": [ "my_cell = BallAndStick(0)\n", "my_other_cell = BallAndStick(1)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Note that this is not equivalent to attaching the `soma` to the `dend`; instead it means that the dendrite begins where the soma ends. We can see that in the topology:" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.113278Z", "iopub.status.busy": "2025-08-18T03:35:41.113136Z", "iopub.status.idle": "2025-08-18T03:35:41.118894Z", "shell.execute_reply": "2025-08-18T03:35:41.118533Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "|-| BallAndStick[0].soma(0-1)\n", " `| BallAndStick[0].dend(0-1)\n", "|-| BallAndStick[1].soma(0-1)\n", " `| BallAndStick[1].dend(0-1)\n", "\n" ] }, { "data": { "text/plain": [ "1.0" ] }, "execution_count": 21, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.topology()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "For now, we can get rid of `my_other_cell`:" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.122651Z", "iopub.status.busy": "2025-08-18T03:35:41.122502Z", "iopub.status.idle": "2025-08-18T03:35:41.127470Z", "shell.execute_reply": "2025-08-18T03:35:41.127085Z" } }, "outputs": [], "source": [ "del my_other_cell" ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.129567Z", "iopub.status.busy": "2025-08-18T03:35:41.128901Z", "iopub.status.idle": "2025-08-18T03:35:41.136841Z", "shell.execute_reply": "2025-08-18T03:35:41.136464Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "|-| BallAndStick[0].soma(0-1)\n", " `| BallAndStick[0].dend(0-1)\n", "\n" ] }, { "data": { "text/plain": [ "1.0" ] }, "execution_count": 23, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.topology()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "A `soma` can have many dendrites attached to it, but any dendrite only begins at one specific location." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "What if we didn't want to attach the dendrite to the end of the soma (position 1)? We could explicitly specify the connection location via, e.g. `self.dend.connect(self.soma(0.5))` which would mean the dendrite was attached to the center of the soma. (Recall: segments are described using normalized positions.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The 1 end of the soma is said to be the parent of the `dend` section." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Define stylized geometry" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's set the length and the width for both sections. We'll make the soma have length and diameter of 12.6157 microns, the dendrite have length 200 microns and diameter 1 micron." ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.138636Z", "iopub.status.busy": "2025-08-18T03:35:41.138490Z", "iopub.status.idle": "2025-08-18T03:35:41.144515Z", "shell.execute_reply": "2025-08-18T03:35:41.144141Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self, gid):\n", " self._gid = gid\n", " self.soma = n.Section(\"soma\", self)\n", " self.dend = n.Section(\"dend\", self)\n", " self.dend.connect(self.soma)\n", " self.soma.L = self.soma.diam = 12.6157 * µm\n", " self.dend.L = 200 * µm\n", " self.dend.diam = 1 * µm\n", "\n", " def __repr__(self):\n", " return \"BallAndStick[{}]\".format(self._gid)\n", "\n", "\n", "my_cell = BallAndStick(0)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If you're wondering why that number was chosen for the soma length and diameter: it is because it makes the surface area (which doesn't include end faces) approximately 500 μm2:" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.145965Z", "iopub.status.busy": "2025-08-18T03:35:41.145822Z", "iopub.status.idle": "2025-08-18T03:35:41.151005Z", "shell.execute_reply": "2025-08-18T03:35:41.150631Z" } }, "outputs": [ { "data": { "text/plain": [ "500.00296377255506" ] }, "execution_count": 25, "metadata": {}, "output_type": "execute_result" } ], "source": [ "my_cell.soma(0.5).area()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "(NEURON only returns areas of segments which is why we asked for the center `soma` segment; since there is only one segment, the area here is the same as the whole Section area.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Note that the surface area of a cylinder with equal length and diameter\n", "$$\n", "\\pi d \\ell = \\pi d^2 = 4 \\pi \\left (\\frac{d}{2} \\right) ^2 = 4 \\pi r^2\n", "$$\n", "is the same as the surface area of a sphere with the same diameter." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "That is, if we're only interested in electrophysiology modeling, we can substitute a cylindrical soma with equal length and diameter for a spherical soma with the same diameter, as we've done here. (The volume, however, is of course different. So this substitution does not work if we're modeling diffusion or accumulation of ions.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "For the rest of this tutorial page, we'll focus solely on one cell." ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.154263Z", "iopub.status.busy": "2025-08-18T03:35:41.153692Z", "iopub.status.idle": "2025-08-18T03:35:41.161511Z", "shell.execute_reply": "2025-08-18T03:35:41.159733Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "|-| BallAndStick[0].soma(0-1)\n", " `| BallAndStick[0].dend(0-1)\n", "\n" ] }, { "data": { "text/plain": [ "1.0" ] }, "execution_count": 26, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.topology()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now it is time to see what the cell looks like:" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.164967Z", "iopub.status.busy": "2025-08-18T03:35:41.164819Z", "iopub.status.idle": "2025-08-18T03:35:41.420462Z", "shell.execute_reply": "2025-08-18T03:35:41.420029Z" } }, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " // There's no need to resize if the WebSocket is not connected:\n", " // - If it is still connecting, then we will get an initial resize from\n", " // Python once it connects.\n", " // - If it has disconnected, then resizing will clear the canvas and\n", " // never get anything back to refill it, so better to not resize and\n", " // keep something visible.\n", " if (fig.ws.readyState != 1) {\n", " return;\n", " }\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " buttons: event.buttons,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "" ] }, "execution_count": 27, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import matplotlib.pyplot as plt\n", "\n", "n.PlotShape(False).plot(plt)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We can also make an interactive shape plot in a separate window using NEURON's built-in graphics, via:" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.423743Z", "iopub.status.busy": "2025-08-18T03:35:41.423587Z", "iopub.status.idle": "2025-08-18T03:35:41.437416Z", "shell.execute_reply": "2025-08-18T03:35:41.437067Z" } }, "outputs": [], "source": [ "# enable NEURON's graphics\n", "from neuron import gui\n", "\n", "# here: True means show using NEURON's GUI; False means do not do so, at least not at first\n", "ps = n.PlotShape(True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Either way, you will notice that this looks like a line instead of a ball and stick. Why? It's because NEURON by default does not display diameters. This behavior is useful when we need to see the structure of small dendrites, and in NEURON 7.7, it's the only supported option for Jupyter notebooks with `n.PlotShape`... but when using NEURON's built-in graphics, we can use the show method to show diamters via:" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Why does this look like a line instead of a ball and stick? It's because NEURON by default does not display diameters. This behavior is useful when we need to see the structure of small dendrites, but for now, let's show the diameters:" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.441034Z", "iopub.status.busy": "2025-08-18T03:35:41.440893Z", "iopub.status.idle": "2025-08-18T03:35:41.446509Z", "shell.execute_reply": "2025-08-18T03:35:41.445057Z" } }, "outputs": [ { "data": { "text/plain": [ "1" ] }, "execution_count": 29, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ps = n.PlotShape(True)\n", "ps.show(0)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In Jupyter, we can rotate images by clicking and dragging; we can zoom by right-clicking and dragging. When using NEURON's built-in graphics which appear in separate windows, right-click and select \"3D Rotate\", then drag to rotate. For this simple morphology, there is not anything else more to see." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "(Note: If you want to build your own visualization tool using matplotlib, mayavi, etc, ensure 3D points exist with `n.define_shape()`, then loop over all the sections with `n.allsec()` and read the morphology using `sec.x3d(i)` etc and `sec.diam3d(i)` for `i` in 0, .., `sec.n3d() - 1`. Less efficiently, the (x, y, z; diam) values for a whole section may be read by `sec.psection()['morphology']['pt3d']`.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Specify biophysics" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Our cell needs biophysical mechanisms in the membrane. We start by setting axial resistance and membrane capacitance. (Recall: NEURON's default axial resistance is appropriate for squid but low for mammalian models.)" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.449779Z", "iopub.status.busy": "2025-08-18T03:35:41.448143Z", "iopub.status.idle": "2025-08-18T03:35:41.457479Z", "shell.execute_reply": "2025-08-18T03:35:41.457090Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self, gid):\n", " self._gid = gid\n", " self.soma = n.Section(\"soma\", self)\n", " self.dend = n.Section(\"dend\", self)\n", " self.dend.connect(self.soma)\n", " self.all = self.soma.wholetree() # <-- NEW\n", " self.soma.L = self.soma.diam = 12.6157 * µm\n", " self.dend.L = 200 * µm\n", " self.dend.diam = 1 * µm\n", " for sec in self.all: # <-- NEW\n", " sec.Ra = 100 # Axial resistance in Ohm * cm # <-- NEW\n", " sec.cm = 1 # Membrane capacitance in micro Farads / cm^2 # <-- NEW\n", "\n", " def __repr__(self):\n", " return \"BallAndStick[{}]\".format(self._gid)\n", "\n", "\n", "my_cell = BallAndStick(0)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We've added a new variable `self.all` which is a list of all the sections in the cell. The wholetree method of a Section returns a list of all the sections it is attached to -- i.e. the corresponding neuron. This will help us iterate over them to -- in this case -- specify axial resistance and membrane capacitance, but can also be used for any other biophysics." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This is getting a little complicated. Let's split `__init__` into several functions:" ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.460598Z", "iopub.status.busy": "2025-08-18T03:35:41.460448Z", "iopub.status.idle": "2025-08-18T03:35:41.470074Z", "shell.execute_reply": "2025-08-18T03:35:41.469414Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self, gid):\n", " self._gid = gid\n", " self._setup_morphology()\n", " self._setup_biophysics()\n", "\n", " def _setup_morphology(self):\n", " self.soma = n.Section(\"soma\", self)\n", " self.dend = n.Section(\"dend\", self)\n", " self.all = [self.soma, self.dend]\n", " self.dend.connect(self.soma)\n", " self.soma.L = self.soma.diam = 12.6157 * µm\n", " self.dend.L = 200 * µm\n", " self.dend.diam = 1\n", "\n", " def _setup_biophysics(self):\n", " for sec in self.all:\n", " sec.Ra = 100 # Axial resistance in Ohm * cm\n", " sec.cm = 1 # Membrane capacitance in micro Farads / cm^2\n", "\n", " def __repr__(self):\n", " return \"BallAndStick[{}]\".format(self._gid)\n", "\n", "\n", "my_cell = BallAndStick(0)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "It may not seem like we gained a lot by doing this, but it makes the code a little more self-documenting (e.g. we can see at a glance which parts have to do with defining the morphology) and it divides it into pieces that could be reused in other cells." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We'll put Hodgkin-Huxley (`hh`) kinetics in the soma and specify some parameters:" ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.473921Z", "iopub.status.busy": "2025-08-18T03:35:41.473773Z", "iopub.status.idle": "2025-08-18T03:35:41.522786Z", "shell.execute_reply": "2025-08-18T03:35:41.522404Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self, gid):\n", " self._gid = gid\n", " self._setup_morphology()\n", " self._setup_biophysics()\n", "\n", " def _setup_morphology(self):\n", " self.soma = n.Section(\"soma\", self)\n", " self.dend = n.Section(\"dend\", self)\n", " self.dend.connect(self.soma)\n", " self.all = self.soma.wholetree()\n", " self.soma.L = self.soma.diam = 12.6157 * µm\n", " self.dend.L = 200 * µm\n", " self.dend.diam = 1 * µm\n", "\n", " def _setup_biophysics(self):\n", " for sec in self.all:\n", " sec.Ra = 100 # Axial resistance in Ohm * cm\n", " sec.cm = 1 # Membrane capacitance in micro Farads / cm^2\n", " self.soma.insert(n.hh) # <-- NEW\n", " for seg in self.soma: # <-- NEW\n", " seg.hh.gnabar = (\n", " 0.12 # Sodium conductance in S/cm2 # <-- NEW\n", " )\n", " seg.hh.gkbar = (\n", " 0.036 # Potassium conductance in S/cm2 # <-- NEW\n", " )\n", " seg.hh.gl = 0.0003 # Leak conductance in S/cm2 # <-- NEW\n", " seg.hh.el = (\n", " -54.3 * mV\n", " ) # Reversal potential # <-- NEW\n", "\n", " def __repr__(self):\n", " return \"BallAndStick[{}]\".format(self._gid)\n", "\n", "\n", "my_cell = BallAndStick(0)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "(Note: here we loop over all segments in the soma, even though we only defined one segment. This gives us more general code, that will still work if we change the number of segments later. Always write your model implementations to be independent of the discretization.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Finally, let's insert a passive (leak) current in the dendrite:" ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.525949Z", "iopub.status.busy": "2025-08-18T03:35:41.525802Z", "iopub.status.idle": "2025-08-18T03:35:41.534284Z", "shell.execute_reply": "2025-08-18T03:35:41.533644Z" } }, "outputs": [], "source": [ "class BallAndStick:\n", " def __init__(self, gid):\n", " self._gid = gid\n", " self._setup_morphology()\n", " self._setup_biophysics()\n", "\n", " def _setup_morphology(self):\n", " self.soma = n.Section(\"soma\", self)\n", " self.dend = n.Section(\"dend\", self)\n", " self.dend.connect(self.soma)\n", " self.all = self.soma.wholetree()\n", " self.soma.L = self.soma.diam = 12.6157 * µm\n", " self.dend.L = 200 * µm\n", " self.dend.diam = 1 * µm\n", "\n", " def _setup_biophysics(self):\n", " for sec in self.all:\n", " sec.Ra = 100 # Axial resistance in Ohm * cm\n", " sec.cm = 1 # Membrane capacitance in micro Farads / cm^2\n", " self.soma.insert(n.hh)\n", " for seg in self.soma:\n", " seg.hh.gnabar = 0.12 # Sodium conductance in S/cm2\n", " seg.hh.gkbar = 0.036 # Potassium conductance in S/cm2\n", " seg.hh.gl = 0.0003 # Leak conductance in S/cm2\n", " seg.hh.el = -54.3 * mV # Reversal potential\n", " # Insert passive current in the dendrite # <-- NEW\n", " self.dend.insert(n.pas) # <-- NEW\n", " for seg in self.dend: # <-- NEW\n", " seg.pas.g = 0.001 # Passive conductance in S/cm2 # <-- NEW\n", " seg.pas.e = -65 * mV # Leak reversal potential # <-- NEW\n", "\n", " def __repr__(self):\n", " return \"BallAndStick[{}]\".format(self._gid)\n", "\n", "\n", "my_cell = BallAndStick(0)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If we weren't sure about the units for a given mechanism’s parameter, use units(). Pass in a string with the paramater name, an underscore, and then the mechanism name. e.g." ] }, { "cell_type": "code", "execution_count": 34, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.537685Z", "iopub.status.busy": "2025-08-18T03:35:41.537539Z", "iopub.status.idle": "2025-08-18T03:35:41.540481Z", "shell.execute_reply": "2025-08-18T03:35:41.540108Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "S/cm2\n" ] } ], "source": [ "print(n.units(\"gnabar_hh\"))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We can use `psection` to see what is present where:" ] }, { "cell_type": "code", "execution_count": 35, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.541877Z", "iopub.status.busy": "2025-08-18T03:35:41.541742Z", "iopub.status.idle": "2025-08-18T03:35:41.550546Z", "shell.execute_reply": "2025-08-18T03:35:41.550156Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "BallAndStick[0].soma: hh\n", "BallAndStick[0].dend: pas\n" ] } ], "source": [ "for sec in n.allsec():\n", " print(\"%s: %s\" % (sec, \", \".join(sec.psection()[\"density_mechs\"].keys())))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "(A quick aside about `psection`: it's great for quickly getting information when interactively exploring a model because it provides a lot of data in one pass; for the same reason, however, other solutions that only extract specific desired information are more efficient for automatic explorations.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Instrumentation" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We have now created our neuron. Let's stimulate it and visualize its dynamics." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Stimulation" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We'll inject a current pulse into the distal (1) end of the dendrite starting 5 ms after the simulation starts, with a duration of 1 ms, and an amplitude of 0.1 nA. First, let's define and position the current clamp object:" ] }, { "cell_type": "code", "execution_count": 36, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.552447Z", "iopub.status.busy": "2025-08-18T03:35:41.552240Z", "iopub.status.idle": "2025-08-18T03:35:41.555303Z", "shell.execute_reply": "2025-08-18T03:35:41.554942Z" } }, "outputs": [], "source": [ "stim = n.IClamp(my_cell.dend(1))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If we want, we can check the segment the current clamp is inserted into:" ] }, { "cell_type": "code", "execution_count": 37, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.557729Z", "iopub.status.busy": "2025-08-18T03:35:41.557585Z", "iopub.status.idle": "2025-08-18T03:35:41.563309Z", "shell.execute_reply": "2025-08-18T03:35:41.562941Z" } }, "outputs": [ { "data": { "text/plain": [ "BallAndStick[0].dend(1)" ] }, "execution_count": 37, "metadata": {}, "output_type": "execute_result" } ], "source": [ "stim.get_segment()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Recall that if we forget what the names of the attributes are, we can check the `dir`. Here we do that and ignore Python-created attributes:" ] }, { "cell_type": "code", "execution_count": 38, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.564950Z", "iopub.status.busy": "2025-08-18T03:35:41.564812Z", "iopub.status.idle": "2025-08-18T03:35:41.570537Z", "shell.execute_reply": "2025-08-18T03:35:41.570150Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "amp, baseattr, delay, dur, get_loc, get_segment, has_loc, hname, hocobjptr, i, loc, same\n" ] } ], "source": [ "print(\", \".join(item for item in dir(stim) if not item.startswith(\"__\")))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The parameters we need to set for a current clamp are `delay` (measured in ms), `dur` (measured in ms), and `amp` (in nA):" ] }, { "cell_type": "code", "execution_count": 39, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.573805Z", "iopub.status.busy": "2025-08-18T03:35:41.573665Z", "iopub.status.idle": "2025-08-18T03:35:41.577014Z", "shell.execute_reply": "2025-08-18T03:35:41.576412Z" } }, "outputs": [], "source": [ "stim.delay = 5\n", "stim.dur = 1\n", "stim.amp = 0.1" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Recording" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We'll start out recording the membrane potential at the center of the soma and the time in two NEURON Vectors:" ] }, { "cell_type": "code", "execution_count": 40, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.580678Z", "iopub.status.busy": "2025-08-18T03:35:41.580536Z", "iopub.status.idle": "2025-08-18T03:35:41.583587Z", "shell.execute_reply": "2025-08-18T03:35:41.583242Z" } }, "outputs": [], "source": [ "soma_v = n.Vector().record(my_cell.soma(0.5)._ref_v)\n", "t = n.Vector().record(n._ref_t)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Run the simulation" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We initialize membrane potential everywhere to -65 mV:" ] }, { "cell_type": "code", "execution_count": 41, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.587011Z", "iopub.status.busy": "2025-08-18T03:35:41.586863Z", "iopub.status.idle": "2025-08-18T03:35:41.593164Z", "shell.execute_reply": "2025-08-18T03:35:41.592817Z" } }, "outputs": [ { "data": { "text/plain": [ "1.0" ] }, "execution_count": 41, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.finitialize(-65 * mV)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now we run until time 25 ms:" ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.596206Z", "iopub.status.busy": "2025-08-18T03:35:41.596065Z", "iopub.status.idle": "2025-08-18T03:35:41.607899Z", "shell.execute_reply": "2025-08-18T03:35:41.607490Z" } }, "outputs": [ { "data": { "text/plain": [ "0.0" ] }, "execution_count": 42, "metadata": {}, "output_type": "execute_result" } ], "source": [ "n.continuerun(25 * ms)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Plot the results" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "As in the scripting neuron basics part of the tutorial, we initialize `bokeh` graphics:" ] }, { "cell_type": "code", "execution_count": 43, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:41.609476Z", "iopub.status.busy": "2025-08-18T03:35:41.609316Z", "iopub.status.idle": "2025-08-18T03:35:42.176952Z", "shell.execute_reply": "2025-08-18T03:35:42.176588Z" } }, "outputs": [ { "data": { "text/html": [ " \n", "
\n", " \n", " Loading BokehJS ...\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "'use strict';\n", "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " const force = true;\n", "\n", " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", " root._bokeh_onload_callbacks = [];\n", " root._bokeh_is_loading = undefined;\n", " }\n", "\n", "const JS_MIME_TYPE = 'application/javascript';\n", " const HTML_MIME_TYPE = 'text/html';\n", " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", " const CLASS_NAME = 'output_bokeh rendered_html';\n", "\n", " /**\n", " * Render data to the DOM node\n", " */\n", " function render(props, node) {\n", " const script = document.createElement(\"script\");\n", " node.appendChild(script);\n", " }\n", "\n", " /**\n", " * Handle when an output is cleared or removed\n", " */\n", " function handleClearOutput(event, handle) {\n", " function drop(id) {\n", " const view = Bokeh.index.get_by_id(id)\n", " if (view != null) {\n", " view.model.document.clear()\n", " Bokeh.index.delete(view)\n", " }\n", " }\n", "\n", " const cell = handle.cell;\n", "\n", " const id = cell.output_area._bokeh_element_id;\n", " const server_id = cell.output_area._bokeh_server_id;\n", "\n", " // Clean up Bokeh references\n", " if (id != null) {\n", " drop(id)\n", " }\n", "\n", " if (server_id !== undefined) {\n", " // Clean up Bokeh references\n", " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", " cell.notebook.kernel.execute(cmd_clean, {\n", " iopub: {\n", " output: function(msg) {\n", " const id = msg.content.text.trim()\n", " drop(id)\n", " }\n", " }\n", " });\n", " // Destroy server and session\n", " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", " cell.notebook.kernel.execute(cmd_destroy);\n", " }\n", " }\n", "\n", " /**\n", " * Handle when a new output is added\n", " */\n", " function handleAddOutput(event, handle) {\n", " const output_area = handle.output_area;\n", " const output = handle.output;\n", "\n", " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", " return\n", " }\n", "\n", " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", "\n", " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", " // store reference to embed id on output_area\n", " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", " }\n", " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", " const bk_div = document.createElement(\"div\");\n", " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", " const script_attrs = bk_div.children[0].attributes;\n", " for (let i = 0; i < script_attrs.length; i++) {\n", " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", " }\n", " // store reference to server id on output_area\n", " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", " }\n", " }\n", "\n", " function register_renderer(events, OutputArea) {\n", "\n", " function append_mime(data, metadata, element) {\n", " // create a DOM node to render to\n", " const toinsert = this.create_output_subarea(\n", " metadata,\n", " CLASS_NAME,\n", " EXEC_MIME_TYPE\n", " );\n", " this.keyboard_manager.register_events(toinsert);\n", " // Render to node\n", " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", " render(props, toinsert[toinsert.length - 1]);\n", " element.append(toinsert);\n", " return toinsert\n", " }\n", "\n", " /* Handle when an output is cleared or removed */\n", " events.on('clear_output.CodeCell', handleClearOutput);\n", " events.on('delete.Cell', handleClearOutput);\n", "\n", " /* Handle when a new output is added */\n", " events.on('output_added.OutputArea', handleAddOutput);\n", "\n", " /**\n", " * Register the mime type and append_mime function with output_area\n", " */\n", " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", " /* Is output safe? */\n", " safe: true,\n", " /* Index of renderer in `output_area.display_order` */\n", " index: 0\n", " });\n", " }\n", "\n", " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", " if (root.Jupyter !== undefined) {\n", " const events = require('base/js/events');\n", " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", "\n", " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", " register_renderer(events, OutputArea);\n", " }\n", " }\n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " const NB_LOAD_WARNING = {'data': {'text/html':\n", " \"
\\n\"+\n", " \"

\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"

\\n\"+\n", " \"
    \\n\"+\n", " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", " \"
\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded(error = null) {\n", " const el = document.getElementById(\"d68b6bc6-380d-4d8d-8009-a89649737eea\");\n", " if (el != null) {\n", " const html = (() => {\n", " if (typeof root.Bokeh === \"undefined\") {\n", " if (error == null) {\n", " return \"BokehJS is loading ...\";\n", " } else {\n", " return \"BokehJS failed to load.\";\n", " }\n", " } else {\n", " const prefix = `BokehJS ${root.Bokeh.version}`;\n", " if (error == null) {\n", " return `${prefix} successfully loaded.`;\n", " } else {\n", " return `${prefix} encountered errors while loading and may not function as expected.`;\n", " }\n", " }\n", " })();\n", " el.innerHTML = html;\n", "\n", " if (error != null) {\n", " const wrapper = document.createElement(\"div\");\n", " wrapper.style.overflow = \"auto\";\n", " wrapper.style.height = \"5em\";\n", " wrapper.style.resize = \"vertical\";\n", " const content = document.createElement(\"div\");\n", " content.style.fontFamily = \"monospace\";\n", " content.style.whiteSpace = \"pre-wrap\";\n", " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", " content.textContent = error.stack ?? error.toString();\n", " wrapper.append(content);\n", " el.append(wrapper);\n", " }\n", " } else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(() => display_loaded(error), 100);\n", " }\n", " }\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete root._bokeh_onload_callbacks\n", " }\n", " console.debug(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(css_urls, js_urls, callback) {\n", " if (css_urls == null) css_urls = [];\n", " if (js_urls == null) js_urls = [];\n", "\n", " root._bokeh_onload_callbacks.push(callback);\n", " if (root._bokeh_is_loading > 0) {\n", " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", "\n", " function on_load() {\n", " root._bokeh_is_loading--;\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", " run_callbacks()\n", " }\n", " }\n", "\n", " function on_error(url) {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " for (let i = 0; i < css_urls.length; i++) {\n", " const url = css_urls[i];\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error.bind(null, url);\n", " element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " }\n", "\n", " for (let i = 0; i < js_urls.length; i++) {\n", " const url = js_urls[i];\n", " const element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error.bind(null, url);\n", " element.async = false;\n", " element.src = url;\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.7.2.min.js\"];\n", " const css_urls = [];\n", "\n", " const inline_js = [ function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", "function(Bokeh) {\n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " if (root.Bokeh !== undefined || force === true) {\n", " try {\n", " for (let i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", "\n", " } catch (error) {display_loaded(error);throw error;\n", " }if (force === true) {\n", " display_loaded();\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " } else if (force !== true) {\n", " const cell = $(document.getElementById(\"d68b6bc6-380d-4d8d-8009-a89649737eea\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\n", " }\n", "\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(css_urls, js_urls, function() {\n", " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(window));" ], "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(\"d68b6bc6-380d-4d8d-8009-a89649737eea\");\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.7.2.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {display_loaded(error);throw error;\n }if (force === true) {\n display_loaded();\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(\"d68b6bc6-380d-4d8d-8009-a89649737eea\")).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from bokeh.io import output_notebook\n", "import bokeh.plotting as plt\n", "\n", "output_notebook()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "(If you prefer to use `matplotlib` graphics, you can adapt the code below using the examples in the scripting neuron basics part of the tutorial.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now we plot membrane potential vs time:" ] }, { "cell_type": "code", "execution_count": 44, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:42.179069Z", "iopub.status.busy": "2025-08-18T03:35:42.178753Z", "iopub.status.idle": "2025-08-18T03:35:42.904549Z", "shell.execute_reply": "2025-08-18T03:35:42.904129Z" } }, "outputs": [ { "data": { "text/html": [ "\n", "
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(root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1001" } }, "output_type": "display_data" } ], "source": [ "f = plt.figure(x_axis_label=\"t (ms)\", y_axis_label=\"v (mV)\")\n", "f.line(t, soma_v, line_width=2)\n", "plt.show(f)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We have a cell that responds to input, so that's good, let's explore the role of some parameters to see what they do and see if we can get an action potential." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Simulation studies" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Role of current amplitude" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's do a set of simulations, plotted in the same figure, where we vary the amplitude of the current in a `for` loop:" ] }, { "cell_type": "code", "execution_count": 45, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:42.908811Z", "iopub.status.busy": "2025-08-18T03:35:42.906206Z", "iopub.status.idle": "2025-08-18T03:35:43.058795Z", "shell.execute_reply": "2025-08-18T03:35:43.058411Z" } }, "outputs": [ { "data": { "text/html": [ "\n", "
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" const render_items = [{\"docid\":\"dc535127-93d0-42f6-ad33-9c3e6f791907\",\"roots\":{\"p1044\":\"b805d0b3-9b37-4546-ab9d-d15a7738bf7e\"},\"root_ids\":[\"p1044\"]}];\n", " void root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1044" } }, "output_type": "display_data" } ], "source": [ "f = plt.figure(x_axis_label=\"t (ms)\", y_axis_label=\"v (mV)\")\n", "amps = [0.075 * i for i in range(1, 5)]\n", "colors = [\"green\", \"blue\", \"red\", \"black\"]\n", "for amp, color in zip(amps, colors):\n", " stim.amp = amp\n", " n.finitialize(-65 * mV)\n", " n.continuerun(25 * ms)\n", " f.line(t, list(soma_v), line_width=2, legend_label=\"amp=%g\" % amp, color=color)\n", "plt.show(f)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The `for` loop syntax as used here is looping over amplitude, color pairs. The only potential \"gotcha\" here is the need to make a copy of the values by passing in `list(soma_v)` instead of `soma_v`. If this copying was omitted, only the last set of values would be plotted." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Plotting both the dendrite and the soma" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "To plot the dendrite potential, we need to record it in a NEURON Vector:" ] }, { "cell_type": "code", "execution_count": 46, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:43.062216Z", "iopub.status.busy": "2025-08-18T03:35:43.061935Z", "iopub.status.idle": "2025-08-18T03:35:43.067034Z", "shell.execute_reply": "2025-08-18T03:35:43.066669Z" } }, "outputs": [], "source": [ "dend_v = n.Vector().record(my_cell.dend(0.5)._ref_v)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Note that we do not need to reassign the existing time and soma membrane potential recording vectors." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The running and plotting code is very similar to the above; the only difference is one additional call to the `line` method to plot the `dend_v` using a dashed line without a separate legend entry:" ] }, { "cell_type": "code", "execution_count": 47, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:43.071501Z", "iopub.status.busy": "2025-08-18T03:35:43.068456Z", "iopub.status.idle": "2025-08-18T03:35:43.275824Z", "shell.execute_reply": "2025-08-18T03:35:43.275414Z" } }, "outputs": [ { "data": { "text/html": [ "\n", "
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[0.075 * i for i in range(1, 5)]\n", "colors = [\"green\", \"blue\", \"red\", \"black\"]\n", "for amp, color in zip(amps, colors):\n", " stim.amp = amp\n", " n.finitialize(-65 * mV)\n", " n.continuerun(25 * ms)\n", " f.line(t, list(soma_v), line_width=2, legend_label=\"amp=%g\" % amp, color=color)\n", " f.line(t, list(dend_v), line_width=2, line_dash=\"dashed\", color=color)\n", "\n", "plt.show(f)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We see that when the soma membrane potential is sufficiently low, it is possible for the dendrite to be more depolarized than the soma, but the peak membrane potential in the leaky dendrite is significantly reduced from the peak in the soma during an action potential. (This is because in our model all the voltage-gated channels that would depolarize the cell are only present in the soma.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### The role of nseg" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's see the effects of nseg, the number of segments of the dendrite, on the signal through the dendrite." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We'll do this by modifying the above code to run all of our simulations for both `nseg = 1` (the default) and for `nseg = 101`. We'll use thin lines for the high resolution (`nseg = 101`) case and thick lines for the low resolution case:" ] }, { "cell_type": "code", "execution_count": 48, "metadata": { "execution": { "iopub.execute_input": "2025-08-18T03:35:43.278071Z", "iopub.status.busy": "2025-08-18T03:35:43.277760Z", "iopub.status.idle": "2025-08-18T03:35:43.649862Z", "shell.execute_reply": "2025-08-18T03:35:43.649401Z" } }, "outputs": [ { "data": { "text/html": [ "\n", "
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Tool\",\"id\":\"p1263\"}]}},\"left\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1246\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1247\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1248\"},\"axis_label\":\"v 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" const render_items = [{\"docid\":\"7eb27da4-7713-402f-b3db-420c74220098\",\"roots\":{\"p1230\":\"e5b796e4-3ab8-47a2-b0d5-6a168a29a379\"},\"root_ids\":[\"p1230\"]}];\n", " void root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1230" } }, "output_type": "display_data" } ], "source": [ "f = plt.figure(x_axis_label=\"t (ms)\", y_axis_label=\"v (mV)\")\n", "amps = [0.075 * i for i in range(1, 5)]\n", "colors = [\"green\", \"blue\", \"red\", \"black\"]\n", "for amp, color in zip(amps, colors):\n", " stim.amp = amp\n", " for my_cell.dend.nseg, width in [(1, 2), (101, 1)]:\n", " n.finitialize(-65)\n", " n.continuerun(25)\n", " f.line(\n", " t,\n", " list(soma_v),\n", " line_width=width,\n", " legend_label=\"amp={:.3g}\".format(amp) if my_cell.dend.nseg == 1 else \"\",\n", " color=color,\n", " )\n", " f.line(t, list(dend_v), line_width=width, line_dash=\"dashed\", color=color)\n", "plt.show(f)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This code has only two changes to the previous code: (1) addition of the `for` loop for `dend.nseg` values and width with accompanying indentation changes, (2) a modification to the legend formula to only generate a legend for the `nseg=1` case since the colors are unchanged. (The calls to `f.line` are split onto multiple lines but this is only for readability; there is no difference to Python if it is on one line or on multiple lines.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Here we see with the high-resolution simulation that the soma peaks should be reduced and delayed and the dendrite peaks increased relative to what was seen in the `nseg=1` case." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Exercise\n", "\n", "Modify the above example, increasing the low resolution case from `nseg=1` to find a low value of `nseg` that gives negligible error relative to the high-resolution `nseg=101` case. Hint: a non-quantitative way to proceed would be to find values such that all the thin and thick curves of a given color overlap. (Note that since we're plotting from the center of the dendrite, `nseg` should be odd, otherwise the center will fall on the segment boundaries and be ill-defined.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Advanced exercise" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Calculate the approximate absolute error for your low `nseg` solution that graphically overlaps the high `nseg` solution. Compare this to the error for the `nseg=1` case. (Since the true solution is unknown, approximate it with the high `nseg` solution.)" ] } ], "metadata": { "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.12.10" } }, "nbformat": 4, "nbformat_minor": 2 }