Maximum Intensity Projections in Amira 5.4

(A) Setting Up Your Environment to Run Amira

1. Amira can currently only be run from jane, so you will first need to ssh to jane:

$ ssh -Y jane.crbs.ucsd.edu

2. Enter the directory that contains your reconstruction. For example:

$ cd /ccdbprod/ccdbprod2/home/CCDB_DATA_USER.portal/CCDB_DATA_USER/acquisition/project_20191/microscopy_87042/reconstruction 

3. Start Amira:

$ /ncmir/local.linux.amd64/Amira-5.4/bin/start

If you want, you can setup your login script to alias this command to the command 'amira'. To do this, add the following line to your .bashrc file by editing it in a text editor (vi, emacs, nano, etc.):

alias amira='/ncmir/local.linux.amd64/Amira-5.4/bin/start'

If you do this, the next time you use Amira, you will only have to type the command 'amira' rather than the full path.

Pool --> Open Data --> Select Data --> MRC Volume

Right click on button --> Display --> Voltex

Left click on Voltex button

Color table

Luminance/alpha

Colormap --> Edit --> Adjust to histogram, then adjust the min and max values accordingly

Alpha scale = 1

Texture mode: 2D

Downsample: 2 2 2

Apply