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.

Basic data

u.enter.tiltSeries(fileWorkshop);
u.enter.tiltAngles(-57:3:60);
u.enter.discardedTiltIndices([1,2,40]); 

Acquisition settings

u.enter.settingAcquisition.apix(2.7);

Detection settings

These here are the actual design decisions when running an alignment workflow:

u.enter.settingDetection.beadRadius(16); u.enter.settingDetection.maskRadius(28);

u.enter.templateSidelength(64);

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.

u.enter.settingDetection.detectionBinningFactor(1);

Detection settings

u.enter.settingComputing.parallelCPUUse(1);

Changing generic parameters

Yo can find handles to the parameters of the individuals steps through auto ompletion on the area, then step items.

u.area.indexing.step.tiltGapFiller.parameterSet.residualsThreshold(8);

% computing parameters

Running the workflow

u.run.all('noctf',1);