Link to this page: bit.ly/openneuroscience

Link to this page

Activity 1: Cellular anatomy of the nervous system

Click on a link to one of the serial electron micrograph (EM) brain volumes below to enter the Neuroglancer visualizer. The left side of the window will show the EM view and the right side will show a 3D reconstruction of selected cell(s). The first volume below (Mouse cortical layer 2/3) is the easist to navigate and get used to the Neuroglancer interface. So, it is recommended that you begin there first, and then move on to additional volumes as you become more comfortable. Click on the “?” button in the upper right corner of the Neuroglancer window and review the keyboard and mouse shortcuts that will allow you to navigate through the volume.

The following are some of the most common navigation tools you will frequently use:

  • Single mouse click: put the focus on a view of interest (e.g., the EM view on the left or the 3d reconstruction on the right)
  • Double mouse click: toggle a cell or process on or off
  • Scroll wheel or pinch on mousepad: zoom in or out (first place the mouse cursor over the view you wish to zoom in and out of)
  • Ctrl = and Ctrl -: zoom in and zoom out (first single mouse click on the view you wish to zoom in and out of)
  • comma and period: change z plane down and up, respectively (only works when EM view is selected)
  • You can also change the x,y, and z locations manually in the upper left corner of the window
  • l (lower case l): recolor (changes all segment colors, it is not specific for one cell; see below)
  • Ctrl-A: toggle crosshairs off and on
  • Single click on a layer rectangle (on top of window): toggle the view of that layer on or off
  • Right click on a layer rectangle: open up options box for that layer (for example, reduce the opacity in 3D view as necessary to improve visualization of internal features, or change the color of a particular cell, among other settings)
  • Click on icons in upper right corner of a view to change between single window, split window, and quad window view

Instructions

Beginning with the Mouse cortical Layer 2/3 volume, spend some time getting comfortable with selecting and navigating neurons, processes, and glia in the volume. Find good examples of the list below, and copy and paste into the document you will submit for this activity: i. a screenshot (shift-cmd-4 on Mac and Print Screen on PC), and ii. Neuroglancer link (instructions for copying the Neuroglancer link are included below for each volume). Be sure to include a brief description and which volume the image is obtained from in your document.

Find the following in at least two different EM volumes (note that several of these will not be seen in the fly volumes):

  • An excitatory neuron (contains spiny dendrites; fly neurons do not have spines)
  • Zoom in on a spine and find a synapse; select the pre-synaptic process/neuron (note that there are many processes that do not have the soma in the volume); be sure the EM view you take clearly shows synaptic vesicles in the pre-synaptic process and the post-synaptic density in the post-synaptic cell
  • A primary neuronal cilia (look on neurons with their full soma in the volume)
  • An inhibitory neuron (generally do not have spines on dendrites)
  • An astrocyte
  • A blood vessel
  • An interesting or unusual feature you found (this is easier to find in the fly volumes since invertebrate cells are markedly different from mammalian cells)
  • Optional (more of a challenge): find a microglia, oligodendrocyte or OPC cell

Having trouble? See a list of cell ids by cell subtype in the mouse cortex Layer 2/3 volume to help you along. Also, try the gallery links below to help you find certain types of cells in the respective volumes.

1. Mouse cortical Layer 2/3 volume (Microns Consortium): Layer 2/3

2. Full adult fly brain (Janelia/Google): FAFB-FFN1

  • View interesting visualizations in the FAFB-FFN1 Gallery
  • To copy the Neuroglancer link, select the entire URL in the browser (use Ctrl-A to select all) and paste the link to your document.

3. Fruit Fly hemibrain volume (Janelia/Google): FlyEM hemibrain

  • To copy the Neuroglancer link, select the entire URL in the browser (use Ctrl-A to select all) and paste the link to your document.

4. Mouse cortex one cubic mm volume (Microns Consortium): mm^3

  • View interesting visualizations in the mm^3 Gallery
  • To copy the Neuroglancer link, select the entire URL in the browser (use Ctrl-A to select all) and paste the link to your document.

5. Human cortex volume (Harvard/Google): H01

  • View interesting visualizations in the H01 Gallery
  • To copy the Neuroglancer link, select the entire URL in the browser (use Ctrl-A to select all) and paste the link to your document.

Activity 2: Modeling resting membrane potential and action potentials

A simple, PhET interactive neuron model is available from the University of Colorado Boulder PhET website.

PhET neuron simulation: https://phet.colorado.edu/sims/html/neuron/latest/neuron_en.html

Follow the instructions and complete the activities in the handout that your teacher or professor provides.

Some helpful tips for using the simulation:

  • Keep in mind that this simulator does not show negatively charged ions and focuses only on sodium and potassium ions and channels.
  • You may find it helpful to zoom in to the membrane using the + button in the upper left.
  • When first familiarizing yourself with the simulation control, you may find it helpful to use the “Fast Forward” setting, and then using the “Normal” and “Slow Motion” settings when trying to understand the dynamics of an action potential.
  • It is useful to always show charges and concentrations (click the checkbox for show “Charges” and “Concentrations”); click Show “Potential Chart” when you want to observe the membrane potential before, during, and after an action potential (otherwise keep it unchecked).
  • Press the “Stimulate Neuron” button to initiate an action potential.
  • Press the pause, back and forward buttons to stop and step through single frames when you want to observe the rapid ion changes during the simulation.

Be sure to write your name on your paper before turning it in at the end of the lab activity.

Activity 3: Neural network simulator

An interactive neural network simulator developed at the University of Oslo and hosted at the Neuronify website.

Neuonify: https://dragly.org/projects/neuronify/

Before starting, familiarize yourself with Neuronify:

  • If the simulation freezes and becomes unresponsive, hit the reload button on your browser (you will lose whatever you were working on).
  • Read through the 3 tutorials (click “Next tutorial” to go to the next one).
  • Under “New” in the upper left corner, go through each of the “Neuronify Items” (skip the “Visual input” one since we won’t use that item).

Look at the following pre-made neural networks:

  • Under New > Textbook Examples, look at Lateral Inhibition 1 and Summation examples.
  • Under New > Miscellaneous, look at Direction Selective Network, Feedback Inhibition, Reciprocal Inhibition, and Disinhibition

How to create a new simulation (blank canvas):

  • Under New, select “New simulation”

How to save a simulation that you have created (in order to turn in for credit):

  • Press the “Save as” button in the upper left
  • The Neuronify file will automatically download as simulation.nfy (you will need to rename this in your file manager)

Simulations you will create and submit to your instructor in your LMS (e.g., Canvas)

Create the following reflex circuits:

  1. Patellar reflex circuit (hitting the patellar tendon with a reflex hammer)
  2. Crossed extension reflex (stepping on a thumbtack)

On both of these circuits, use the annotation tool to label each neuron by name and type (sensory or motor), whether it is excitatory or inhibitory. For sensory neurons, include the type of receptor (e.g., pain, stretch, etc.) and for motor neurons, identify the target muscle by name.

See a diagram of the patellar reflex and crossed extension reflex circuits here on doctorlib

Once you have successfully built both circuits:

  • Take a screenshot of each circuit and submit the image files as part of your assignment submission (e.g., on Canvas)
  • Be sure the screenshot clearly shows the Measurement diagram (e.g., voltmeter) and the voltmeter has traces that demonstrate the circuit is working properly (hint: hit the Pause button in the simulator in order to freeze the traces so you can take a screen capture)
  • Save the Neuronify file with the following filename: patellar_reflex_yourname.nfy and extension_reflex_yourname.nfy
  • Submit the Neuronify files as part of the assignment submissions as well (e.g., on Canvas)