https://github.com/jefferis/pnvisualisationinamira

Examples of how to visualise groups of Projection Neurons in Amira
https://github.com/jefferis/pnvisualisationinamira

Last synced: 27 days ago
JSON representation

Examples of how to visualise groups of Projection Neurons in Amira

• Host: GitHub
• URL: https://github.com/jefferis/pnvisualisationinamira
• Owner: jefferis
• Created: 2011-07-22T16:57:47.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2015-08-25T02:32:19.000Z (about 9 years ago)
• Last Synced: 2023-04-16T09:10:57.063Z (over 1 year ago)
• Language: Haxe
• Homepage:
• Size: 7.18 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# PNVisualisationInAmira

Scripts and data to compare different groups of Drosophila olfactory projection neurons in Amira

![images](doc/Montage5x2.png)

## Installation

Use the **Download ZIP** button and expand or clone the repository to a sensible location.

## Loading data into Amira

1. Open **masterObject.scro** in Amira (you can do this by drag and drop or double clicking).

2. Click on the **LoadAll** button

3. Now you can click on the **HideAll**/**ShowAll** button to hide or show all neurons

## Changing the display

1. You can select groups of neurons using the check boxes

2. You can change the colour of the currently selected neurons with the **Red**, 

   **Green** and **Blue** sliders

3. You can also change the **Width**

## Colouring neurons programmatically

You can colour all of the neurons from a single glomerulus by going to Amira's

Console and issuing a command of the form:

```

DM3 setrgb 1 1 .4 

```

An example of doing this for all glomeruli is presented in [`setneuroncolors.hx`](amira/setneuroncolors.hx).

You can drag and drop this script onto the Amira object pool and it will set all

of these colours.

## Snapshots

To make a series of snapshots, INSTRUCTIONS are at the top [`makesnapshots.hx`](amira/makesnapshots.hx).

## Further Information

Contact Greg or see flybrain.stanford.edu for more details.