Note: This exercise was adapted from work done at the University of Minnesota, which developed the content with funding from the National Institutes of Health.
In this exercise you will use the NeuroMorpho.Org database to compare morphological data from multiple neurons of different brain regions and different species, including elephants, lobsters and flies. NeuroMorpho is a huge, free database that contains 3D renderings and data from thousands of digitally reconstructed neurons contributed from over 100 laboratories worldwide. These are not micrographs of neurons, but rather digital tracings of axons and dendrites. First, you will learn to navigate and explore NeuroMorpho and, then, you will select 6 neurons from different brain regions and species. When selecting your neurons make sure to include at least two invertebrates (e.g. drosophila—fruitfly or c. elegans—nematode worm), and at least two of the same type of neuron from two different species (e.g. Purkinje neurons from elephants and mice).
Part I - Exploration
In a web browser, visit this web page: http://www.neuromorpho.org You may browse through the files or conduct a search using options from the orange menu bar just above the neuron images and text on the home page. Try each of these ways to access the neuron data:
1. Click on BROWSE. There are 4 ways in which the files are organized: by animal species, by brain region, by cell types, and by lab name.
2. Click on SEARCH by in the same menu. You may search by Metadata, Morphometry, or Keywords. In Keyword search you type into a text box and press Enter or Return. Click Show Summary to see your results or click on one of the buttons above that to sort your data by species, brain region, or cell type.
Try BROWSE by animal species to see a colorful pie chart showing the species and the number of neuron reconstructions for each collection. Click on an area of the pie chart and hover over items in the resulting list to see an image of the neuron in a pop-up window:
If you click on the file name - for example, 10-2911-XDCT-s1-cell1 - you'll get a page of details and can view the 3D animation. The reconstruction is color coded as follows: white (soma), gray (axon), green (basal dendrite), magenta (apical dendrite). You will also see a list of data associated with that specific neuron.
Part II - Data Collection and Recording
You will need to make sketches for this assignment. Choose the option below that best suits your needs. Ideally, we would like all of your work submitted as one assignment as either a .doc, .docx, or .pdf.
1. Download the following worksheet: NeuralStructureVLab.doc
2. Save the worksheet on your computer and rename it: LastName.FirstName.NStructureVLab.doc
3. Keep the worksheet open and toggle back and forth between http://www.neuromorpho.org and the worksheet, making sure to fill in the tables and answer the questions.
Note: To add images (.jpg, .png, .tiff, etc.) to a Word document, click 'Insert' and choose photo. For more detailed instructions from Microsoft, click here.
4. Click 'Submit Assignment' and upload your completed worksheet on this assignment page.
1. Open 'Google Docs'. (You must have a google account first. To set up a Google account, click here.)
2. Create a new 'Document'.
3. Click here and then cut and paste the assignment questions into your new Google doc. and enter your answers.
Note: To add images (.jpg, .png, .tiff) to a Google document, click 'Insert' and choose photo. For more detailed instructions from Google, click here.
4. When you are finished with your work, use the 'File' menu to rename the document as LastName.FirstName.NStructureVLab and download it as a .pdf.
5. Click 'Submit Assignment' and upload your completed worksheet on this assignment page as .pdf.
Note: The NeuroMorpho.Org site has many more features than those included in this activity. Visit their FAQs (under HELP on the main menu or at www.neuromorpho.org/neuroMorpho/myfaq.jsp) for answers and to learn more about this terrific resource.