Manual

Table of Contents

Introduction

The Microscope Simulator is a program for simulating the imaging process of various microscopes. Currently, simulation of atomic force microscopes (AFM) and fluorescence microscopes is supported through the AFMSim and FluoroSim modules. These modules enable you to see what a geometric model of specimen would look like in one of these microscopes with given imaging parameters. Graphics acceleration hardware allows real time generation of simulated microscope images while you interact with specimen models.

Among other things, you can use the Microscope Simulator to build intuition about the artifacts that arise in the imaging process of each microscope, test and refine a hypothesized model by comparing output from the simulator to experimental images, and check whether your microscope can distinguish among several hypothetical specimen model configurations.

The Microscope Simulator consists of a unified modeling environment for setting up specimen models. Controls for setting properties of the microscope simulators are split into two different modules, AFMSim for AFM simulation and FluoroSim for fluorescence microscope simulation. This page describes the modeling environment and features common to both simulators. See AFMSim and FluoroSim for more information on each simulator's features.

Installation

The Microscope Simulator is currently available only for PCs running Microsoft Windows XP. The installer for the Microscope Simulator 1.3.1 can be found here. Install the program by either running the application or downloading it to disk and double-clicking the installer.

If you have not installed other software from the UNC Nanoscale Science Research Group before, this installer will create the folder "C:\NSRG" by default. We recommend accepting the default installation settings to ensure that the program works correctly. If you have installed this version of the Microscope Simulator before, we advise that you remove the previous version first; installing different versions of the Microscope Simulator on the same machine should not cause problems. The installer will create menu items under Start->All Programs->NSRG->Microscope Simulator 1.3.1. These items include:

Program Window

Program window after startup
The program window after startup. The program window, shown on the right, consists of several panels. At the top of the window is a standard menu bar. Below the menu bar is the Microscope Control Panel where settings for the microscopes can be edited. The large blue panel in the center of the window is the Model Display Panel where specimen models are shown. Rotating, translating, and scaling models interactively with the mouse takes place in this window. A row of icons above the Model Display Panel controls how specimen models appear and whether simulation results are displayed along with the models. The Model Object Control Panel on the right consists of two parts; the Model Object List at the top displays a list of models in the simulation, and the Model Object Properties Panel at the bottom displays a list of model properties that can typically be edited. Each of these panels is described in more detail below.

Menu Bar

The menu bar in the Microscope Simulator contains three menus that provide commands useful to creating new simulations, adding specimen models to a simulation, saving simulations, and loading saved simulations. Each menu is described in more detail below.

File Menu

File Menu
The File menu. The File Menu features typical options for creating and saving simulations:

New
Creates a new simulation with default settings.
Open...
Opens a saved simulation file.
Save
Saves a simulation's settings to a file. This includes the settings of each microscope simulator, the objects in the scene and their settings, and everything else required to recreate the simulation. If the simulation has not been saved previously, you will be asked to provide a name and location for the file.
Save as...
Does the same thing as the Save menu item, but allows you to save the simulation to another file name.
Export UNCA
Exports simulated AFM scans to the UNCA file format.
Exit
Exit the program.

Model Menu

Model Menu
The Model menu. The model menu has options for adding and removing geometric models to the simulation.

Add Disk
Adds a model of a planar disk defined by the center of the disk and a radius.
Add Flexible Tube
Adds a model of tube defined by several control points and a radius. The number of control points can be changed, and each control point can be specified independently.
Add Nanotube
Adds a model of a carbon nanotube. The ends of the model are capped with spherical ends. The length and radius of the tube can be changed.
Add Plane
Adds a simple bounded planar model to the scene.
Add Point Set
Adds a point set that allows explicit settings of fluorophore positions. No geometry is involved, but the points are represented by small spheres in the Model Object Window.
Add Sphere
Adds a sphere to the scene. The radius of the sphere can be adjusted.
Add Torus
Adds a torus to the scene. The radius of the torus and the radius of the cross-section can be adjusted independently.
Import Fluorescence Stack
Imports a series of TIFF files representing a stack from a fluorescence microscope. The origin, pixel size, and interslice spacing can be set according to the settings from the microscope.
Import OBJ File
Imports a 3D geometric mesh described in OBJ file format. The OBJ format is commonly supported in many 3D modeling and graphics programs. The scale of the OBJ file can be modified.
Import PLY
Imports a 3D geometric mesh described in PLY file format. The PLY format is also commonly supported in many modeling programs.
Import UNCA File
Imports a UNCA file describing a height field from an atomic force microscope scan. The UNCA file format was developed at UNC. Data in the nanoManipulator system can be exported to UNCA format an imported into the Microscope Simulator with this menu item.
Import VTK Poly Data File
Imports a legacy VTK file containing a vtkPolyData structure that describes a surface mesh.
Clear
Clears all models from the simulation.

Window Menu

Window Menu
The Window menu. The Window menu has just two options:

Show Fluorescence Window
This menu item brings up the Fluorescence Image window that shows images generated by the FluoroSim module.
Preferences...
Brings up a dialog box for changing program preferences. Preferences are saved between program launches.
About
Shows information about this program.

Microscope Simulator preferences panel
The Microscope Simulator preferences panel. There are currently just two preferences supported. The first sets the background color in the Model Display Panel. The second determines whether a grid is displayed on the ground plane.

Microscope Control Panel

Microscope Control Panel
The Microscope Control Panel with the AFMSim tab selected. The Microscope Control Panel has three tabs that bring up settings for the two microscope simulators. Controls for general settings common to both microscope simulators are also found under the General tab. Further information about the settings for each microscope simulator can be found under the AFMSim and FluoroSim pages.

Model Display Panel

The Model Display Panel is where the 3D models in the simulation are displayed. Output from the microscope simulator modules can also be displayed in this window. Such output includes simulated AFM scans displayed at the base of the simulation environment and simulated fluorescence images displayed on a physical representation of the focal plane.

Visualization Icons

Icon row
The visualization icons. A row of visualization icons provide various controls related to what is shown in the Model Display Panel. The functions represented by the icons are described from left to right below:

Save image
Save the image currently displayed in the Model Object Panel.
Reset camera
Reset the scene to the default view.
Just one of the following visualization modes can be enabled at a time:
View model only
Displays specimen models only.
View fluorophore sampling
Displays fluorophores from models in the scene as small spheres.
View models with AFM scan
Displays both the specimen models and the simulated AFM surface scan.
View AFM scan only
Displays the simulated AFM surface scan only.
View models with fluorescence comparison
Displays comparison of experimental and simulated fluorescence image stacks with the models visible. See the section on processing simulated stacks for more details on the comparison visualization.
View fluorescence comparison only
Display comparison of experimental and simulated fluorescence image stacks without the models visible. See the section on processing simulated stacks for more details on the comparison visualization.
Toggle reference axes
Enables/disables display of coordinate axes in the Model View Panel. The location of the coordinate axes can be moved to an arbitrary location in the Model View Panel display by clicking on the axes and dragging them.

Only one of the following interaction modes can be enabled at a time.

Move camera
Enables manipulation of the camera in the Model View Panel via mouse manipulation. You can change the view of the specimen models by rotating, translating, and zooming in on the scene. Clicking and dragging while holding various mouse buttons enacts these camera transformations:
  • Left mouse button - Causes rotation of the scene
  • Middle mouse button - Causes translation of the scene
  • Right mouse button - Causes zooming in on the scene
Move objects
Enables manipulation of individual specimen model objects via mouse manipulation. Clicking on the desired model object and dragging while holding one of the mouse buttons produces the following transformations:
  • Left mouse button - Causes rotation of the selected model object
  • Middle mouse button - Causes translation of the selected model object
  • Right mouse button - Causes different changes dependong on the model object selected. In most cases, scales the size of the model object.

Model Object List

Model Object List
The Model Object List (upper panel) showing one object. Properties for the selected model object appear in the Model Object Properties Panel (lower panel). The model object list appears in the upper right of the program window. All model objects in the simulation are listed here. When you click on a model object in the list, properties for that model object appear in the Model Object Properties Panel. Right-clicking on a model object brings up a context menu that provides several options:

Focus on Object
Changes the camera view to center on this model object and zoom in on it so that it nearly fills the Model Object View Panel.
Snap Simulated Region to Object
Changes the spatial extent of the simulation (defined in nanometers under the General tab in the Microscope Control Panel) to just contain this model object.
Export Geometry
Exports the model object geometry as a VTK, PLY, or BYU file.
Delete Object
Deletes this model object.
Clear
Clears all model objects from the simulation.

Model Object Properties Panel

The Model Object Properties Panel lists the properties of a model object in the left column and the property values in the right column. Most model object properties can be changed in this panel. A few properties common to almost all model objects are listed here:

Name
A name for the model object.
Visible
Controls whether the model object is visible in the scene or not.
Scannable
Controls whether the model object is included when calculating a simulated AFM scan.
X
X-component of the model object position.
Y
Y-component of the model object position.
Z
Z-component of the model object position.
X-rotation
X-component of the model object rotation (in degrees).
Y-rotation
Y-component of the model object rotation (in degrees).
Z-rotation
Z-component of the model object rotation (in degrees).
Color
The color used to represent the model object. Does not affect simulations.
Surface Fluors
The model of fluorophores on the model object surface.
Volume Fluors
The model of fluorophores in the volume defined by the model object surface.

Some model objects have fewer properties. For example, the sphere model does not have the rotation properties because a sphere's shape is rotationally invariant. Other models have more properties, such as the Ring Radius and Cross Section Radius in the torus model. Still other models have a variable number of properties. The flexible tube model, for example, supports an arbitrary number of control points.

Version History

The sections below outline the changes made to the Microscope Simulator at each revision.

Version 1.3.1

Changes from previous release

Known issues

Version 1.3.0

Changes from previous release

Known issues

Version 1.2.2

Changes from previous release

Known issues

Version 1.2.1

Changes from previous release

Known issues

Version 1.2.0

Changes from previous release

Known issues

Version 1.1.0

Changes from previous release

Known issues

Version 1.0.8

Changes from previous release

Known issues

Version 1.0.7

Changes from previous release

Known issues

Version 1.0.6

Changes from previous release

Known issues

Version 1.0.5

Changes from previous release

Known issues

Version 1.0.4

Changes from previous release

Known issues