Exercise 1

Author: pgleeson

Exercises/Exercise1_NeuroMorpho_to_OSB.md

@@ -1,16 +1,34 @@
-## Cell morphology from NeuroMorpho visualised on Open Source Brain
+## Cell morphology from NeuroMorpho.Org visualised on Open Source Brain
 
 ### Local software requirements
 
-None, apart from an up to date web browser 
+None, apart from an up to date web browser.
 
 ### Instructions
 
-1. Download morphology from Neuromorpho in NeuroML 2 format
+#### 1. Download morphology from NeuroMorpho.Org in NeuroML 2 format
 
 Pick a cell, e.g. [this one](http://neuromorpho.org/neuron_info.jsp?neuron_name=A1-May29-IR2-3-G)
 
- - Set up user account on GitHub
+![NeuroMorpho](images/neuromorpho.png)
+
+Select **3D Neuron Viewer**. This will show a 3D view of the cell in an external 
+window (Java Applet, see below if you have issues). Select in **Save as** the option
+to download in NeuroML2 format.
+
+![3D View](images/3Dview.png)
+
+If the 3D Neuron Viewer does not open you may have to change your setting to allow 
+Java Applets to run. See: *"The 3D Neuron Viewer does not launch. What can I do?"* [here](http://neuromorpho.org/myfaq.jsp).
+
+For Mac you may need to specify where the Java Web Start is located (to run the jnlp file). 
+When it asks which application to open with, navigate to the root directory (not 
+Applications), go to "System" -> "Library" -> "CoreServices" and pick "Java Web Start".
+
+If there is still an issue, just download the SWC version of the morphology (via **Morphology File (Standardized)**)
+or get a copy of the NeuroML 2 file [here](files/A1-May29-IR2-3-G.cell.nml).
+
+#### 2. Set up user account on GitHub
 
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