Walkthrough on command line based tilt series alignment
This is the command line based version of the GUI based alignment walkthrough
Create the workflow
name = 'hivCommandLine'; folder = 'workflows'; u = dtsa(name,'--nogui','-path',folder,'fp',1);
Here, we instruct Dynamo to skip opening the GUI. We also create the workflow in a different folder.
Entering the data
The u object contains several areas to interact with the workflow. They can be found by autocompletion using the tab key.
u.enter.tiltSeries(fileWorkshop); u.enter.tiltAngles(-57:3:60); u.enter.discardedTiltIndices([1,2,40]);
These here are the actual design decisions when running an alignment workflow:
The bin level is mainly used to accelerate the detection procedure. Needs to be chosen in a way that a binned gold bead still can be recognisable as such, with a radius of at least 4 pixels.
Changing generic parameters
Yo can find handles to the parameters of the individuals steps through auto ompletion on the area, then step items.
% computing parameters
Running the workflow