ImageVis3D User`s Manual
Contents
1. ImageVis3D User s Manual NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop Po 1 The current state of ImageVis3D P rototy ping Alpha Basic features GL Rendering Core Field Testing _DX Rendering Core Beta Field Testing Additional Features Testing Release Candidates 1 0 Release Remember 1 If ImageVis3D causes any kind of trouble please report this to us 2 We are still in the process of adding features to the 1 0 release so please give us your input NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop Se 2 Tutorial 2 1 Settings Configuration and User Interface 2 1 1 Initial Configuration The first time you start ImageVis3D it will ask you to configure some default settings As this is the first time you ve started ImageVis3D on this system you need to Ea configure the initial settings In particular the memory usage settings need to be configured according to the hardware configuration of the machine Mote that these settings can be changed later in the settings screen OK After selecting OK ImageVis3D presents you with the settings window This consists of 4 tabs Memory Performance User Interface and Renderer The most important of these are the Memory and Renderer tabs which contain compatibility settings to make ImageVis3D work with your graphics card 2 1 1 1 Memory Tab ImageVis3D contains advanced memory management2. The Open files without verification checkbox is off by default and it is probably a good idea to leave it as such ImageVis3D verifies that the data you load are not corrupt so you can be sure you are viewing exactly what you saved last week or your colleague saved before sending you However this process can be slow and so if you are opening the same file repeatedly it can be nice to disable that check The four sliders allow control of ImageVis3D s interactivity at the expense of raw performance Minimal framerate is a target framerate that ImageVis3D will try to maintain at all times Active Timeslice and Inactive Timeslice have the largest effect on interactivity they control how often ImageVis3D will check to see if you are changing rendering parameters Larger timeslices will lower total rendering time but may cause ImageVis3D to feel as if it lags behind your input ImageVis3D achieves interactivity using multiple level of detail LOD settings A typical scenario for scientists using visualization software is configuring a particular viewpoint transfer function or other rendering parameters such that the feature of interest is visible or prominent While interacting with the software it can be a nuisance to do a complete render every time some small setting is changed because a complete render can take quite some time and many more changes will need to be made before settling on a final rendering LOD techniques allow us t
3. FIREWORKS Tuvok 0 04 beta Windows 32bit build E Y O N mae C Wore HE fersion 0 04 beta HREWORKS Tuvok 0 04 beta Windows 32bit build rey 1 0 Load Workspace Rendermode Save Workspace DVRA 1D Transfer function P Reset Workspace DVR 2D Transfer Function P Rendering Options Progress Viewer 1D Transferfunction Editor 2D Transferfunction Editor Isosurface Settings Render Settings Lighting Global Bounding Box Locking Options Local Bounding Box Recorder O Sampling Stereo What you get is a new UI item floating around freely on your desktop it is not restricted to the ImageVis3D canvas Try to drag this Item to the borders of your ImageVis3D window and you will see that it attaches itself to the borders Now open a second UI item from the Workspace menu say the Progress viewer and also attach that to a border Next detach the Rendering Options item and attach it on the same border as the Progress Viewer You may notice that you can do multiple things with the Ul items such as put them on top of each other allowing you to see only one at a time or one under the other where you can see both simultaneously given that your window is large enough To hide a UI item you can either close it with the X button or whatever the close button looks like on your operating system or by deselecting it in the Workspace menu 2 1 3 Opening a dataset What s a rende
4. this mode you can hit space again over any of the four sub windows to enlarge that window Using the mouse over the 3D will behave just like with the large view while using the mousewheel over the small views scrolls through the slices Try to hit x and y over the slice views to flip the x and y Axes m will switch between the slice view and a maximum intensity projection Next let us load another dataset this time pick the tooth uvf file In ImageVis3D you do not need to close the c60 view as it can handle arbitrarily many windows well actually only up to 2 4 294 967 296 but that should be sufficient for most users Now also play with the tooth dataset You can also select Clone current view from the view menu to create another view to the same dataset 2 2 Transfer Functions 2 2 1 1D Transfer Functions Now let us change the way the dataset is rendered first by playing with the 1D transfer function First open the 1D Transfer function Editor from the Workspace menu 1D Transferfunction Editor ia Copy to 2D Now right click and drag the mouse in the black box and watch the dataset change Now left click and draw into the box and see how you can fine tune your transfer function The color channels to modify are selectable on the left and the slider on the right controls the scale of the NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop histogram You can also sa
5. and then add or remove stops to the gradient or click on a stop to change its color and opacity Note that if editing of the 2D Transfer function is slow on your system you may want to switch to the On Release or the Manual Execution mode in the Rendering Options UI item Also enable disable the lighting to see the unlit Transfer function only dataset 2 2 3 lsusurfacing To simply look at a particular isosurface select the Isosurface Settings from the Workspace menu NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop First enable the lsosurfacing with the checkbox and then move the slider to select a specific isovalue Use the Choose Color button to change the color of your isosurface select a dark blue Now enable the ClearView technology by clicking on the second checkbox Now you can select a second isovalue Next move your cursor over the 3D view of you dataset and hold the shift key As you can see the ClearView lens moves over your data To change the appearance of the ClearView lens use the three sliders on the bottom 2 3 Rendering Features 2 3 1 Rotations ImageVis3D can generate a set of images from a 360 rotation around the volume of interest To do this select the Recorder Image from the Workspace menu The filename listed gives both the capture png format and base name for the generated image files in the example here ImageVis3D will generate capture0 png S
6. code to make sure it does not attempt to exceed the capabilities of your system To effectively perform that task it must know what those capabilities are Memory Performance User Interface Renderer Memory Usage GPU Memory E 412 MB CPU Memory je OS SSE MB Statistics CPU Mem 6746 MB 7074734080 bytes GPU Mem unchecked Processors unchecked Running in 64 bit mode The GPU Memory slider tells ImageVis3D how much memory you have on your graphics card Mac OS X users can obtain this information from the System Profiler Linux users can normally NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop glean the amount of video memory from var log Xorg 0 log The CPU Memory slider controls the amount of system RAM ImageVis3D will assume it can access all of this while it runs For this reason especially if you re running many other applications it can be a good idea to set the CPU Memory a bit lower than your system s actual available RAM It is not so bad if you set these sliders a bit too low but it can effect performance severely if you set them too high Thus if you are unsure you should utilize conservative settings It is essentially unheard of for any GPU to have less than 64mb of memory these days likewise most systems purchased in the last 3 years have a gigabyte 1024 MB of memory or more 2 1 1 2 Performance Tab The Performance tab lets you customize the interactivity of ImageVis3D
7. graphics cards but Raycasting gives better quality Blend Precision tells ImageVis3D how much detail to retain when rendering 8 bit is supported across all graphics cards but recent GPUs support 76 bit or even 32 bit blending which will generate higher quality images Use only power of 2 textures should be enabled on all but the most modern graphics cards without it ImageVis3D will perform poorly Avoid Compositing is necessary to work around defects in some GPUs GPU drivers If an image seems to disappear into the background arbitrarily or you notice polygons which seem to pop and flicker as you rotate the volume you will need this setting Unfortunately this currently disables ImageVis3D s ClearView rendering mode 2 1 2 The Idea behind the ImageVis3D UI Memory Performance User Interface Renderer Render Method Render API e Slicing Raycasting OpenGL Directs Blend Precision 6 Bit 16 Bit 32 Bit Compatibility Lise only power of 2 textures Avoid Compositing Color Background Select Top Color Select Bottom Color Logo Mo Logo Selected Select File Top Left Top Right Bottom Left Bottom Right Cancel None ImageVis3D has a very flexible and highly customizable interface so let us first explore the Ul When you open ImageVis3D all you see is an empty canvas NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop T ImageVis3D Version 0 04 beta
8. ingle Sequence capture1 png etc Click the Capture button and a dialog will appear which queries for the number of images Note that the images will always represent a 360 rotation regardless of the Capture number of images Recorder E Gx Full Rotation 2 3 2 MIP ImageVis3D can also render MIP images including MIP rotations To use this feature first hit space to get a 2x2 panel view of different viewpoints File Edit View Workspace Help Qt 1 Aocalh hometfogaltmp UVF hand16 uvf O x Then hover your mouse over the plane you are interested in and hit space again to make that projection the only active one Finally hit m to switch into MIP rendering mode File Edit View Workspace Help File Edit View Workspace Help CH 1 docalhomestfogaltmp UVFMhand 16 0 x MN 1 JocalhomesfogaltmpUVFhand16 uvf o x aad wf You can also generate MIP rotations by using the Recorder window as shown earlier When selecting capture you will be presented with some extra configuration options eee USI Orthographic Projection is probably the Number of images per rotation projection most people use when Pa i 36 10 per image generating MIP rotations Stereo creates stereo MIPs Renderer e Orthographic Projection Perspective Projection 2 3 3 Stereo Stereo ImageVis3D can also generate stereo renderings suitable for viewing using ae anaglyph 3D glasses U
9. o do a quick preview render in this scenario so the user may get an idea of how the completed render will look without committing to the time required for a full render To take advantage of this ImageVis3D monitors how long it has been since the user changed a rendering parameter If it has been long enough then ImageVis3D will load and render a higher resolution portion of the dataset The LOD Delay slider controls how long ImageVis3D will wait 2 1 1 3 User Interface Tab This tab contains settings for what ImageVis3D will remember across runs e Save Workspace on Exit Saves the set of open windows e g the transfer function editors or rendering options windows e Save Window on Exit Which windows were open rendering settings in those windows NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop e Lock cloned Window Whether or not a cloned window has its view parameters locked with the source window e Absolute View Locks Toggles between relative and absolute view locking In both cases rotation in one window will cause rotation in all windows which are locked to that window With relative locking the view parameters are allowed to differ so you could for example view a volume from opposite angles 2 1 1 4 Renderer Tab The Renderer tab contains compatibility and quality settings The Render Method selects the renderer type in general Slicing is compatible across more
10. ring tool without a dataset To open a dataset in ImageVis3D you have two options in the File menu NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop E ImageVis3D Version 0 04 beta FIREWORKS Tuvok 0 04 beta Windows 32bit build Edit View Workspace Help Load Dataset from File Load Dataset from Directory Most Recently Used Quit Load Dataset from File and Load Dataset from Directory the first option loads datasets stored in a single file or files with detached headers e g nrrd raw uvf etc while the second menu item opens an entire directory analyzes the files in that directory groups them into stacks and lets you open those stacks e g images DICOM Now let us open the c60 uvf dataset from the data directory Use the Load Dataset from File menu item and point it to the c60 uvf in the data directory on your stick or on the desktop on our machines You should see an image like this one maybe not as colorful but similar IimageVis3D Play around a little with the dataset for example by changing the size of the window Left click and drag in the window to rotate the dataset right click and drag to move it and use the mousewheel to zoom in or out Now hit space to switch to 2x2 mode and you should see something like this NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop 0 C Users krueger Documents Visual Studio 2008 gt E In
11. sing x Cancel ImageVis3D in this mode will give the illusion of three dimensional volumes Use the Workspace Stereo menu to enable stereo rendering NIH NCRR Center for Integrative Biomedical Computing CIBC Workshop
12. ve your transfer function if you store it in the same directory as your dataset and give it the same name it will be automatically loaded the next time you open the dataset 2 2 2 2D Transfer Functions Next let us explore the 2D transfer functions therefore open the 2D Transfer function Editor from the Workspace menu depending on your screen size you may also want to close the 1D Transfer function Editor now You now see something like this 2D Transferfunction Editor First switch the rendering to 2D Transfer function Rendering by clicking on the checkbox in the top left corner By default the transfer function starts with a single quad unless a premade function was loaded automatically Now select the Quadrilateral in the selection box on the left and shift left click hold the shift key while left clicking and dragging the mouse in the black box on the right to move the quad around Use Ctrl left click to scale the quad and Ctrl Shift left click to rotate it Now use a simple left click to move the nearest vertex yellow of the quad or the endpoints of the gradient green Right click to add a new vertex to the closest edge of the polygon note how the name of the polygon changes on box to the left Right click directly on a vertex to remove it To add another quad or a circle click on the buttons to the left Finally to change the gradient of a polygon select that polygon in the upper left pane
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