How to run manual picking and mask making¶

Manual picking and mask making use GUIs and require user interaction.
When running these at AMI, you can use amibox02 or amibox03.
When you ssh, you need to use the -X flag to tell the terminal to display the GUI.

ssh -X amibox02

Then put the correct path to appion in front of the command, such as /ami/sw/bin/appion.

/ami/sw/bin/appion makestack2.py --single=start.hed --selectionid=1002 --invert --normalized --maskassess=manualrun1 --boxsize=16 --description="test" --projectid=5 --preset=upload --session=10may13l35 --runname=stack7 --rundir=/ami/data00/appion/10may13l35/stacks/stack7 --no-rejects --no-wait --commit --reverse --limit=1 --continue