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User's Manual

Before Using FluoRender:
    FluoRender reads 8-bit multi-page tiff format, and we can convert from manufacturer specific formats with ImageJ.
    An ImageJ macro makes the conversion even easier, for details about the macro, click here.

Instructions for Basic Operations
  1. Click "Open Volume" icon in the toolbar, in the file chooing dialog select the volume dataset (multiple files can be selected at the same time). The selected datasets are loaded in "Data View" (A) window.

  2. To render the loaded datasets in the render viewport, right click the dataset name in "Data View" (A), then choose "Add to...->Render view1" from popup menu. The 3D reconstruction of the volume dataset displays in "Render View" window and the name of the selected dataset is listed in "Sene view" (B) window.

  3. Colors are assigned automatically as red, green, blue, and white, accroding to the order that datasets are added to the viewport. Colors can also be set with the color chooser in the "Tools" window, or simply double-click on the RGB color values and type in R, G, B, W, P, which are shortcuts for preset colors.

  4. Viewport interactions are controled by the mouse. To rotate the view, click and drag with left mouse button; to move the view, click and drag with middle mouse button, or hold down the ctrl key and drag with the left mouse button; to zoom the view, click and drag with right mouse button.

  5. Rendering properties of the volume dataset are displayed in the "Tools" window, and each channel has its own settings. To switch between the channels, click the channel name in "Sene View" window. Settings for rendering properties are discussed in detail below.

  6. To switch render mode, click on the radio buttons (a, b, c) above the render viewport.

  7. To save the rendering results as an image, click "Capture" (d), and enter image file name.

  8. Loaded datasets and their settings can be saved with a FluoRender project file. To save a project file, click the "Save Project" icon in the tool bar and enter project file name.

  9. To open a project file, click the "Open Project) icon in the tool bar, and choose the file. The saved project is loaded with all the datasets and their settings.

    10. Attention:Project file saves loaded datasets by their paths, and fails to open if paths are changed. It is possible to edit the project file with a text editor and modify the paths of the datasets.

Render View Widgets
    Render view widgets are the controls around the "Render View" window, and render view properties are set by these controls.
  1. Layered: A render mode. Similar to most painting packages, channels are rendered layered on top of another, and the rendering order is specified by that of the "Scene View".

  2. Depth: A render mode. Channels of the dataset are rendered with correct spatial coverage according to their depth values.

  3. Composite: A render mode. Channels of the dataset are rendered individually and blended together for the final rendering. It is effective for visualizing signal colocalization.

  4. Capture: Takes a screen shot of current rendering and save as a tiff file.

  5. Background Color: Sets the viewport backgraound color.

  6. Transp. Sorted Layers: Sets the number of layers for "depth peeling". It only takes effect when semi-transparent polygon data are presented, and higher value indicates higher rendering quality for polygon data.

  7. Camera Ctr.: Turns on/off the display of the viewport camera's center of interests.

  8. FPS: Turn on/off the display of rendering frames per second.

  9. Depth Int: Turns on/off the depth attenuation. The slider sets the intensity of the effect.

  10. Zoom: Changes the size of the data in the viewport by moving viewport camera towards or away from the center of interests. It's same with mouse dragging with right mouse button held down, but with more accuracy.

  11. XYZ Rot: Sets viewport camera rotations by XYZ angle inputs. Values can be set by numerical entering or slider, and they are also linked to mouse interactions with the viewport.


Volume Property Settings

    Volume properties are displayed in the "Tools" window, when the name of the dataset is selected in the "Scene View" window. The "Tools" window is dockable, and user can rearrange the window position by dragging its title bar.

  1. Gamma: Controls the shape of the tone curve. Setting a higher value decreases the contrast, with signals of low intensities accentuated, and a lower value increases the contrast, with signals of low intensities suppressed. A low value is usually desired for confocal datasets, as we want to suppress noise, which are often low intensity signals.

  2. Saturation point: Controls the lowest intensity value of the dataset that maps to the highest output intensity. Moving the slider to the left results a steep tone curve, and more output singals are getting saturated.

  3. Luminance: Controls overall brightness of the final rendering by changing the highest output intensity.

  4. Alpha: Controls the transparency of the signals.

  5. Low Shading: Controls the output intensity of the shaded area of protruded structures.

  6. Color: Color of the dataset. Double click to select all the text in the text window. Shortcuts for commonly used colors: R/r - red, G/g - green, B/b - blue, P/p - purple, W/w - white.

  7. XYZ Spacing: Voxel ratios of the volume dataset. Ratios are linked between channels, and settings for one channel effects all channels in the same viewport.

  8. Extract Boundary: Controls how much boundary-like structures are extracted.

  9. Low Threshold: Intensity values of the voxel lower than the setting are cut off from the output. This setting is independent of gamma value setting.

  10. High Threshold: Intensity values of the voxel higher than the setting are cut off from the output. This setting is independent of gamma value setting.

  11. Highlight: Controls the output intensity of the lit area of protruded structures.

  12. Sample Rate: Controls the smoothness of the output rendering.

  13. Save as default: Save the parameter settings as the default, which are applied to volume datasets loaded later.