# Simulating SMLM data¶

Note

Time required: ~10 min.

In this tutorial, you will learn how to simulate SMLM data based on a geometric model.

## Requirement¶

• Software: SMAP installed. Further information can be found on our GitHub site.

Simulating realistic localization data based on a geometric model.

## Main tutorial¶

### Preparation¶

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:

1. Start SMAP (how to?).

2. Load a new instance of the module LocMoFitGUI in tab [ROIs] -> [Evaluate] (see quick start to recap).

3. Uncheck evaluate on in the left panel:

4. Load the particular model and set up the settings for the model parameters:

### Simulation¶

Once the model is loaded, we have to pass it on to the simulation engine provided by SMAP:

1. 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.

• Click Apply.

LocMoFitGUI is successfully loaded if the new button Set model pars shows up.

2. 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:

Note

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.

3. Usually, we have to set up the SMLM properties in tab [SimulateSites]. For simplicity, we keep the default values.

Hint

You can hover over the respective properties in the tab to show their definitions.

4. 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.

Note

How do I keep the simulated data? You can save it through button Save in tab [File]:

This is the end of the tutorial.