Simulating SMLM data¶
Time required: ~10 min.
In this tutorial, you will learn how to simulate SMLM data based on a geometric model.
Simulating realistic localization data based on a geometric model.
You have to load the geometric model for generating localizations. We use LocMoFitGUI as the interface for setting up the model. Here we use the point model
dualRing3D_discrete of the nuclear pore complex (NPC) as an example:
Start SMAP (how to?).
Load a new instance of the module LocMoFitGUI in tab [ROIs] -> [Evaluate] (see quick start to recap).
Uncheck evaluate on in the left panel:
Load the particular model and set up the settings for the model parameters:
Go to [M1] -> [Model], click the drop-down menu (where select the model… is shown), and then select
Once the model is loaded, we have to pass it on to the simulation engine provided by SMAP:
We first connect the engine to the model:
Go to [ROIs]->[Segment], click SimulateSites in the list of plugins:
Click Use LocMoFit and check LocMoFitGUI in the new window.
LocMoFitGUI is successfully loaded if the new button Set model pars shows up.
Click Set model pars. A new window will show up and allow you to specify parameter values. Here we keep the default values so do not have to change anything:
How do I specify parameter values?
For specifying a fixed value, enter it in field Value for a parameter (can be identified in the columns Name, Type, and Model).
For a random value sampled in a defined interval, enter two values (e.g., ‘-15 15’) separated by a space in field Value. In this example, the parameter will be a random value between -15 and 15.
Usually, we have to set up the SMLM properties in tab [SimulateSites]. For simplicity, we keep the default values.
You can hover over the respective properties in the tab to show their definitions.
Click Run in [SimulateSites]. The simulation is done when ‘ROIManager.Segment.SimulateSites finished’ is displayed in the status bar. This usually takes a few seconds:
Now you can explore the overview of the simulated data. You can interact with the overview with a left click or right click. You can deal with the simulated data as with real data.
How do I keep the simulated data? You can save it through button Save in tab [File]:
This is the end of the tutorial.