Electron microscopy Project

Purpose of the System

The Virtual Transmission Electron Microscopy (VTEM) Project aims to educate high school senior students and college freshman in nanotechnologies and give them an access to use online tools which simulate the Transmission Electron Microscopy. Virtual Transmission Electron Microscopy Project is one of the five nanotechnology projects directed by Binghamton University Mechanical Engineering Department and Chemistry Department, and supported by Computer Science Department. The main purpose of the virtual transmission electron microscopy project is to develop an interactive software package demonstrating how TEM works using computer simulation and animation/graphics. Since these devices are expensive (about 1.5 million dollars) students cannot access it. With the virtual transmission electron microscopy project on the other hand, the students will have an opportunity to learn the working principle of the device.

The second purpose to mention regarding the virtual transmission electron microscopy project is the fact that it will present the students an easy to understand and easy to use user interface.

Scope of the System

The virtual transmission electron microscopy project is being implemented for high school students and college freshman. The users of the system will have a capability to click on various parts of the 3D sketch of the device to learn how each part works.

Functionality

This project simulates the working principle of the transmission electron microscopy. The 3D sketch of the system has been created using Google SketchUp. When a user clicks on a part of the 3D image, a pop-up window appears on the screen. The working principle of that part is displayed as a 2D Flash animation.

Software Platforms

Google SketchUp

Google SketchUp is software that can be used to create 3D models. It is used to create the 3D image of the transmission electron microscopy.

To create the virtual transmission electron microscopy’s external surface and cross section models Google SketchUp Version 6.4.112 is used.

Strengths

Google SketchUp is easy to learn and easy to use.

Weaknesses

Hard to work on curved surfaces. As the transmission electron microscopy’s backbone is curved, it took a lot of time to create the model.

Creating External Surface

The electron microscopy has a cylindrical backbone which is created using the Push/Pull button of Google SketchUp.

• Draw a circle using the Circle tool
• Click on the Push/Pull button
• Click on the circle and pull it until it reaches the desired height.

On the right bottom of the page there is a label in which the designer can enter the desired length if the radius of the circle for precise modeling.

Push/Pull tool has been one of the most useful tools while creating both the backbone and the components of the electron microscopy. For rectangular components the same procedure has been followed after drawing a rectangle instead of circle.

To create cones, narrowing/widening cylinders Move/Copy and Offset tools are used.

• Draw cylinder (as described above)
• Draw a circle on the top of the cylinder using the Offset tool. To do this; click on the Offset tool and then click on the top of the cylinder and enter the desired radius size if there is one.
• Click on the Move/Copy tool and then press Alt key on the keyboard and left click on the second circle on the top of the cylinder and move it forward.

Components are created in a separate part of the screen rather than being created directly on the backbone and then moved and rotated to become a part of the backbone using the Move/Copy and Rotate tools. For rotation follow the following steps:

• Select the component with the Select tool
• Click on the Rotate tool and then click on the component. The first click defines the rotation point. In other words, other points on the component will be rotated around that particular point. By clicking, the rotation axis is also be defined.
• Click once more on the component to choose another point.
• Rotate the component. Click once more to stop rotation.

Suppose you are trying to rotate a rectangle. Let its corner coordinates be (10, 10), (10, 50), (100, 10) and (100, 50). If you want to rotate it around (10, 10) along x-axis, you should click on (10, 10) and then to another corner and rotate it as much as you want. The coordinates of the second click does not affect neither the rotation axis nor the rotation angle however choosing corners will provide ease of use of the tool.

Since the electron microscopy is composed mostly of cylindrical and curved surfaces, choosing the rotation axis is difficult. To choose a correct axis, first create a cube (using Push/Pull tool) and then go onto the cube with the Rotate tool without clicking on the cube. As you move over the cube the rotation axis changes. Once you find the right axis click on Shift key on the keyboard and move the mouse over the curved surface that you want to rotate.

Creating Cross Section

This 3D model is created after finishing the model for external surface. Backbone for the external surface is used. Inner part is created in a separate part of the screen and then moved inside the backbone using Move/Copy tool.

Flash and ActionScript

The animations are created using Flash CS4 and the interactivity is provided by ActionScript 2.0

When you open a flash file, you will see a drawing area to draw on, a timeline and a tool box.

The background and each of the electrons are drawn in different layers. The background of the animation is drawn on the first layer. Background consists of the components of the electron microscopy.

Double clicking on the layer name on the timeline allows the designer to change the name of the layer. How long that specific layer will be displayed on the screen is determined by the number of frames it takes in the timeline.

Creating a single electron

• Insert a new layer by right clicking on the previous layer and selecting Insert Layer.
• Right click on the frame, in which you want the electron to show up in the screen, and select Insert Keyframe.
• Click on that frame and select oval tool to draw a circle. Pressing Shift key on the keyboard while drawing the circle helps you to draw a perfect circle instead of an ellipse.
• Select the circle and right click on it. Select Convert to Symbol, give it a name and convert it to a MovieClip by choosing movie clip from the dropdown menu.
• Right click on another frame, in which you want the electron to disappear from the screen, and select Insert Frame.
• Right click on the layer of the electron and select Add Classic Motion Guide. Insert KeyFrame to this guide layer.
• Choose either pencil tool or brush tool to draw the line on which the electron will move along.
• Drag and drop the electron on the beginning of the path.
• Right click on the last frame of the electron and select Create Classic Tween.
• With last frame still selected, drag and drop the electron to the end of the motion guide. It will be easier to move the electron if other layers are locked. Click on the second dot next to the name of the layer to lock a layer.

Creating multiple electrons that move on the same motion guide

Although the electrons move on the same line, they are created in different layers. The first electron, say e1, starts when the timeline shows 1st frame. e2 starts at 5th frame, e3 at 10th frame and so on. Similarly, if e1 ends at 40th frame, e2 ends at 45th and e3 at 50th.

The same electron creation procedure which is described above is followed for each of the electrons. Instead of redrawing the guideline for each electron, the same guideline is copied and pasted to each layer for the electrons to move on the same path.

Adding interactivity

For user interactivity, buttons are created on the background layer.

• Choose Rectangle Tool from the toolbox and draw a rectangle on the background layer.
• Right click on the rectangle to convert it to a Button. Select Convert to Symbol, give it a name and choose Button from the dropdown menu.
• After that step click on the button and hit F9 to reach the actions window. The ActionScript code goes into this window.

Write: on (press){ _root.gotoAndPlay(frameNumber); }

• This code directs the animation to go to the specified frame when it reaches this particular frame in the timeline.
• These are user defined buttons.
• There are also predefined buttons in the common library of actionscript.
• In order to use these buttons, go to the menu and select window -> common libraries -> buttons and choose the type of button that you want to use. In this window, most of the objects are buttons except a few. The ones that you should not choose are the ones that do not have a button symbol next to them, such as Button Assets.
• After choosing the button, drag and drop it on to the layer.
• Then choose the button and hit F9 to go to the actions window to write the actionscript code that you want the button to execute.

The code for the buttons work when a mouse event occurs. Mouse events are on(press), on(release) and so on.

on (release){ _root.gotoAndPlay(1); }

This code lets the animation to go and play the first frame when the user presses the button.

• When a user clicks on a part of the transmission electron microscopy a pop-up window opens and shows the working principle of this part to the user.
• To accomplish that, first create a button. Create either a user defined button or use a predefined button. Then click on the button and go to its actions window.
• On either press event or the release event add code to cause the animation jump to the specified URL.

             on (release){
        	 getURL("webelectron.html", "_blank");
             }

• After creating the animations go to the menu and select file -> publish settings and make sure everything is set to its default value and publish to HTML is selected. Then click publish.
• It will create the HTML version of the animation. You can then put it in your root file and make one link redirect to this specific file. This is done the same way you give a link to a page.

HTML

The web page (Electron Microscopy under http://steflikk6.cs.binghamton.edu/~nano) for the Virtual Transmission Electron Microscopy project is designed using HTML.

Purpose of the Project

It is the continuation of the project that was done in 2009 that serves the same purpose of educating high school students and college freshman.

Scope of the Project

The users of the system will be able to click on various parts of the 3D sketch of the TEM (Transmission Electron Microscope) and experience how each part works.

Functionality

The 3D model of TEM has been created using Google SketchUp 7.0. When the user clicks on a part of the 3D image,animations corresponding to the part that is clicked show up.

Software Platforms

Google SketchUp

Google Sketchup is a 3D software tool that combines a tool-set with a drawing system. You can also make animations using Sketchup. The animations and the models are made using Google Sketchup verison 7.0. It works very similar to frame concept. I chose Google Sketchup for making animation as well because I can check the positions of the electrons to make sure that they are at the desired position.

Strengths

Google SketchUp is easy to learn and easy to use, you can view the model from the point if view that you choose to make sure you placed the items in the right place that they are supposed to be.

Weaknesses

Model:Hard to work on curved surfaces. As the transmission electron microscopy’s backbone is curved, it took a time to create the models.

Animation: The smoothness of the animations was a big problem. I had to add a lot of scenes to make the smoothness.

Creating The Bottom Cone

1. Use the Circle tool to draw a circle on the ground plane. Then use the Line tool to draw a triangle from the origin point to the edge of the circle, up to a point on the blue axis, and then back down to the origin point. You obtained a triangle at this point.

2. Use the Select tool to select the face of the circle. Then select the Follow Me tool and click the face of the triangle.

3. You have a cone!

Creating a single electron

• Go to "Draw" menu in the toolbar and select circle. After you made a selection, draw a circle on the screen where you want place an electron.

• Insert a new layer by clicking on the "+" button in the layers window .

• Select the electron and right click and choose "Entity Info"

• Click on the layer that you want you electron to be seen.

• You can do the same things again for the number of electrons you will use through the animation.

Making the Inner Core of the Microscope

• Select "Arc" tool from the tool set and draw an arc on the ground.

• Select the "Arc" tool again to draw an arc in the inner part of the arc that you drew previously.

• Select "Pencil" tool to join the beginning and end points of the arcs.

• Select "Push/Pull" tool to arrange the height of the microscope

• You have the inner core of the microscope!

Making the Inner Components of the Microscope

Drawing lenses:

• Do the same steps for creating the inner core, but this time do not make it too high using the "Push/Pull" button

• Select "Rectangle" tool to draw a rectangle in the inner part of the shape.

• Again, select "Push/Pull" button to push into the shape to make the lens mark. Do the same step for the opposite side.

• Use "Move" tool to move it into the inner core.

Drawing Specimen/ Aperture

• Select "Circle" tool from the tool set and draw a circle.

• Select "Push/Pull" button to add a height dimension.

• Draw a smaller circle on the shape to show the place where the sample will be placed on.

• Select "Move OR Rotate" tool to carry the shape in the correct position.

Making the Animation

• Go to View -> Animation -> Make Scene to add scenes to your animations. For easiness, before you click on the add scene, make sure you leave electrons (layers) that you want to be seen in that particular scene.

• Adjust the electrons that you want to show in the scene. Make the scenes as similar as possible for a good animation.

• Continue until you reach at the last scene. (Hint: Add the copy of the last scene as another scene so that there is a smooth transition when the animation replays)

• When you are finished, go to File-> Export-> Animation which will export your animation as a ".avi" file

HTML and JavaScript

Used HTML and a little bit of Javascript to show the three different animations of the microscope "Part1", "Part2", "Part3" respectively. I converted them to ".mov" file before I put them on.

The website can be found under [[1]] http://ws.binghamton.edu/me/Zhou/