Walkthrough on command line based tilt series alignment

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Revision as of 12:56, 27 August 2019 by Daniel Castaño (talk | contribs)
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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


Acquisition settings


Detection settings

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

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


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.


Detection settings


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