JavaFX - How to change view in method body

I'm trying to write a code that will simulate sand pile, and I would like to open new window with simulation in another thread. In this case I have to dynamically change view of the 2nd window, but the view waits until the simulate() method ends even if it is run in another thread. What can I do to change view in SandPileApplicationSimulation:run() method body?

Controller class - simulation method:

public class SandPileController {

    @FXML
    public TextField interval;

    @FXML
    public TextField pathToBoard;

    @FXML
    public ChoiceBox<String> sandGenerationMode;

    @FXML
    protected void simulate() {

// you can ignore that 3 lines
        FieldRoleFileParser parser = new FieldRoleFileParser();
        FieldRole[][] fieldRoles = parser.parse(pathToBoard.getText());

        String value = sandGenerationMode.getValue();
       // this construtor is running initializeView method and it is creating new Stage
        SandPileApplicationSimulation sandPileApplicationSimulation = new SandPileApplicationSimulation(fieldRoles,
                Double.parseDouble(interval.getText()),
                SandGenerationMode.valueOf(value));
        Thread thread = new Thread(sandPileApplicationSimulation);
        thread.start();
    }
}

Stage view:

private void initializeView(FieldRole[][] values) {
        Stage stage = new Stage();

        GridPane root = new GridPane();

       //this loops generates some rectangles based on input
        for (int i = 0; i < columnCount; i++) {
            for (int j = 0; j < columnLength; j++) {
                FieldRole fieldRole = values[i][j];
                Rectangle square = new Rectangle(50, 50);
                square.setFill(fieldRole.getColor());
                root.add(square, i, j);
                board[i][j] = new Field(fieldRole, square);
            }
        }

        stage.setScene(new Scene(root));
        stage.show();
    }

run() method (from Runnable) in SandPileApplicationSimulation class - the method wherein I would like to change the view of scene:

@Override
    @SneakyThrows
    public void run() {

        boolean simulationMode = true;
        boolean hasAnyChange = true;

        generateSand(); // <-- this method change the color of some rectangles


        while (hasAnyChange) {

            hasAnyChange = false;

            Thread.sleep(interval);
            hasAnyChange = simulateFrame(simulationMode); // <-- this lane should change the view by changing the color of rectangles 

            simulationMode = !simulationMode;
            generateSand();
        }

    }

I tried to write only the important information; if I forget something, just tell me please. Thanks for your answers.

EDIT: Here is also main application class and fxml file (only main app has it) class:

@Override
    public void start(Stage stage) throws IOException {
        FXMLLoader fxmlLoader = new FXMLLoader(SandPileApplication.class.getResource("view.fxml"));
        Scene scene = new Scene(fxmlLoader.load(), 320, 175);
        stage.setTitle("Sand pile simulation");
        stage.resizableProperty()
                .setValue(false);
        stage.setScene(scene);
        stage.show();
    }

    public static void main(String[] args) {
        launch();
    }

fxml

<VBox alignment="CENTER" spacing="20.0" xmlns:fx="http://javafx.com/fxml"
      fx:controller="pl.umcs.sandpilesimulator.SandPileController">
    <padding>
        <Insets bottom="20.0" left="20.0" right="20.0" top="20.0"/>
    </padding>

    <TextField fx:id="interval">1.0</TextField>
    <TextField fx:id="pathToBoard" promptText="Path to file with board..."/>
    <ChoiceBox fx:id="sandGenerationMode">
        <items>
            <FXCollections fx:factory="observableArrayList">
                <String fx:value="CENTER" />
                <String fx:value="RANDOM" />
            </FXCollections>
        </items>
    </ChoiceBox>
    <Button text="Simulate" onAction="#simulate"/>
</VBox>

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