Appion

h1. Combine Stacks

Use this option if you want to combine stacks you [[Stack Creation|already created]] (for example stacks from two different sessions). Simply select the stacks you want from the list and submit the job.

!http://emg.nysbc.org/attachments/277/Picture_81.png!

h2. General Workflow:

# Check the new combined stack name, output directory path, and enter a description.

# Select the stacks to combine by checking the appropriate check-boxes.  Stacks from different sessions can be combined, and there is not a limit on the number of different stacks that can be combined.

# Click on "Run Combine Stack" to submit to the cluster.  Alternatively, click on "Just Show Command" to obtain a command that can be copied and pasted into a unix shell.

!http://emg.nysbc.org/attachments/313/Picture_42.png!

# If your job has been submitted to the cluster, a page will appear with a link "Check status of job", which allows tracking of the job via its log-file. This link is also accessible from the "1 running" option under the "Combine Stacks" submenu in the appion sidebar.

# Once the job is finished, an additional link entitled "1 complete" will appear under the "Stacks" tab in the appion sidebar. Clicking on this link opens a summary of all RCT volume runs that have been done on this project. 

h2. Notes, Comments, and Suggestions:

# You cannot yet combine stacks of different pixel sizes.  For this, reset the pixel size and box size for your stack, then use the [[Upload Stack|Upload Stack]] tool, followed by combine stacks. 

[[More Stack Tools|<More Stack Tools]] | [[Particle Alignment|Particle Alignment >]]