Edit Volume Options Widget

This widget allows greater control over viewing parameters. It permits different opacity mappings, control over false color, a "Play" mode, and fidelity/speed tradeoffs when in "planes" rendering mode.

Volume Options Menu Items

False Color Toggle

By default, if two images are specified one is displayed in red and the other in green. Wherever they overlap it is whitish. If one image is turned off (using the "Image 1" or "Image 2" button) then the remaining image can be displayed in its color (ie, red or green) or just in grayscale. This toggle controls that choice.

The following 5 choices are useful "presets" for presenting volume data in different ways. They primarily control how image values are used to determine voxel opacity. All the presets set the choice of the lower two options (Brightness and Opacity using Image Values / Opacity using Brightness Values, see below) appropriately. If you manually change this by picking the other option, the affect of the preset choice will change (in a manner which is not described here). We don't recommend you doing this.

Opacity = Brightness

This is probably the most useful preset. It simply means that the opacity of a voxel will depend upon its visible brightness. Brighter voxels are more opaque. Totally black voxels are totally transparent.

Opaque Data

This is similar to "Opacity = Brightness" except that any voxel which is not totally black will be totally opaque. You should probably only use this when the Map-Threshold option is set (see the menu in the Edit Volume Widget) since otherwise dim (but not totally black) voxels will be totally opaque (and hence you will see a lot of black voxels). Also, the left brightness slider should probably be moved up so that a large fraction of voxels are set to 0 (and hence are totally transparent) since otherwise the image volume won't be very sparse and all of the totally opaque voxels will block your view into the interior of the image.

Manual Opacity Control

This is for those daring soles who want to manually control how voxel intensities are mapped to opacity. When it is chosen, the user can manually manipulate the opacity sliders.

Binary Image

Warning: this menu item may not be working correctly yet. This sets both Opacity sliders to 1 and both Brightness sliders to 1. Thus data is rescaled to look either black or white (or red/greed/white if in color mode). This is useful for examining colocalization of two images. The sliders can be "locked" and moved together to examine a binary image but with different thresholds for what is considered black and what white. See also the Color Square menu entry.

RGB Play

Warning: this menu item may not be working correctly yet. Use this if you want to play through z slices, as if you were using Kevin's play or playRGB programs. Typically you would Pause the display and go to the HOME view. Then, after RGB play is picked, you can step through z slices with the z slider arrow keys on the Volume Clipping widget. If you want the slice to be totally opaque (as in play) move both opacity sliders to 0. You can use the Brightness slider to then adjust the brightness of the the slice. You should probably set the right Resolution slider to zero so that you are seeing the slice in the highest resolution possible. This item sets the sliders on the Volume Clipping widget so that only one z slice will be visible. It also sets the system into "z over-ride mode" so that the z slice will be visible regardless of its orientation. All this menu item really does is set both z Volume Clipping sliders to 0 and locks them together. It also sets what is called "z override" mode. This mode is usually only used when viewing single slices. To make sure that z override mode is turned off, use the Default Values menu item when you are through with RGB Play mode. This will undo everything.

The following two options control whether the opacity sliders (which control how voxel intensity is mapped to opacity) get applied to the voxel values before they are remapped by the brightness sliders, or after the remapping. NOTE: The correct option is automatically chosen when you choose one of the above presets for the opacity sliders. Only manually pick these items if you want to override the default. Doing so will change the operation of the default presets to an undescribed operation.

Brightness and Opacity using Image Values

This choice means that the opacity mapping is based upon the original image values (i.e., before they are remapped by the brightness sliders).

Opacity using Brightness Values

This choice means that the opacity mapping is based upon the remapped image values (i.e., after they are mapped by the brightness sliders). This choice may not be functional yet.

The following two options control the function mapping data values to brightness (or color) values.

Linear RGB Scaling

A data value of x (after being rescaled 0-255 and by the brightness slider settings) gets mapped to a display intensity of x.

Quadratic RGB Scaling

A data value of x (after being rescaled 0-255 and by the brightness slider settings) gets mapped to a display intensity proportional to x*x. The linear option tends to be perceived as saturating very quickly (much before x = 255). This option causes the intensity values to rise more slowly initially so that the mapping looks more linear and doesn't saturate as quickly (see the color square from the Edit Volume menu). Unfortunately, for some reason it also seems to make the dark voxels more visible which is usually undesireable. This may be easily fixed - we haven't tried to track it down yet.

Custom Volume Colormap

If you want to display your voxel data volume using a custom colormap (instead of the gray, green, and red colormaps provided as defaults), choose "Custom Colormap" on the Edit Volume menu. This option, by default, assumes that you have loaded your custom colormap (using Load Map from the Goodies menu on the Master widget) into colormap 15. If you have loaded your colormap into a different map, you should pick this menu item. It lets you type in the new map number.

Sliders and Buttons

Opacity Sliders

These sliders control how opaque the data will be. Normally you should never have to touch these sliders unless you have specified "Manual Control" from the menu. Unless Manual Control is picked, these sliders will move automatically. Think of the image data as a cloud. These sliders control how far into the cloud you can see. Opacity is based upon voxel intensity, the brighter a voxel the more opaque it will be. By default, the intensity used is the image intensity BEFORE the Brightness Sliders get applied. This default setting is depicted with a check mark in the box by "Brightness and Opacity using Image Values" in the menu. See below for more details. In a dual-wavelength image, opacity is based upon the brighter of the two voxel values. See "Map - Rescale" in the main Edit Volume widget for more details on how the remapping of opacity is performed (it is done the same way as the brightness remapping). NOTE: The only computers which permit partial opacity are the GTX, Graphics, Invitro, and Invivo. On the others, voxels are either opaque or transparent. The arrows beside the sliders move the sliders by 1 or 5 units. The LOCK button above the sliders locks them so that they move in tandem.

ABS Slider/REL Slider

These sliders allow one to trade-off image update speed with image fidelity. This only affects performance when rendering in PLANES mode (the default - see Render Options below). The ABS slider specifies the absolute intensity error the user is willing to tolerate in the interest of increasing update speed. The REL slider specifies the relative intensity error (e.g., .10 = 10%) that will be tolerated. By default neither of these tolerances is exceeded (i.e., a voxel is drawn if ABS OR REL is exceeded). If the OR/AND toggle button is changed to AND, then one tolerance may be exceeded but not both (i.e., a voxel is drawn if ABS AND REL are exceeded). Typically an ABS of 10 and a REL of .10 will result in a doubling of update rate with little image degradation - but this is very dependent upon the image and the settings of the Opacity and Brightness sliders. The Volume Debugging widget available from the menu in the Edit Volume Widget will show what the percent speedup is if you are interested. NOTE: when performing a Colocalization Analysis (from the Goodies menu in the DAVE Master Widget) the image may look very funny when in planes mode (long horizontal streaks may appear). You should change to CUBES mode if this occurs.

OR/AND Toggle

See the description of the ABS and REL sliders above.

Average Button/Maximum Button/Median Buttons

These buttons control how the lower resolution images are calculated from the initial image. Each voxel in a lower resolution image is gotten from the values of 8 voxels (2 by 2 by 2) in the higher resolution image. If Maximum is chosen then the low resolution voxel's intensity will be set to the maximum of the 8 voxels. Average sets it to the average of the 8 values, and median (not currently operational) will set it to the median value. Average will tend to make the lower resolution images look dimmer (and hence also more transparent) when the image is sparse. Maximum will make images look brighter and will also make Red/Green overlap look greater (when two images are present).