Brightness and color (and opacity) - ekatrukha/BigTrace GitHub Wiki
You can show "Brightness and Color" dialog panel by using shortcut S:
This is an example of the dialog showing settings for two channels.
It uses range sliders (and one can pull the range by dragging the middle interval).
The range of each slider (min/max) is shown on the right and can be adjusted by right-clicking on the numbers.
The squared icon on the left is used to assign a single color (left click) or FIJI's lookup table (LUT, right click) to the specific channel.
The main "brightness" range slider maps image intensity values to the specific color/LUT range.
By clicking on the "three triangles" button, each channel's panel can be expanded to show advanced settings.
By default the first range slider maps intensity linearly.
This mapping can be changed to non-linear mode by adjusting the second "γ" slider below, introducing gamma value (a power-law).
In addition to color (LUT) mapping, one can also independently change the opacity of voxels using the alpha "α range" (with a corresponding "γ α" gamma adjustment slider below).
Using these sliders, the opacity/transparency can be specified independently, so it is decoupled from the color.
This feature is useful mostly for volumetric rendering and not so much for maximum-intensity projection.
A checkbox on the left is used to synchronize the change in the top pair of sliders (color LUT) with the bottom pair (α and "γ α"), but not the other way around (see video below).
When you open an image in the beginning, it is usually helpful to find a proper intensity interval/gamma when they are synchronized and later fine-tune the opacity.
Visibility & Grouping
An alternative way to change brightness/contrast for one or multiple channels or to switch some sources on/off is to use the Cards panel on the right side of BigVolumeViewer canvas. This panel can be extended using shortcut P (and collapsed with ⌃ Ctrl + P).
Or using hidden arrow at the middle of the right edge of the canvas.
By default Display mode "Fused" mode shows all active channels (otherwise just current).
You can toggle channel (source) visibility with corresponding checkboxes at the Sources inset. It can be handy to focus on one channel at a time. A similar brightness/contrast panel per one source is displayed at the bottom of the inset.
Groups panel inset allows you to create a group of sources/channels and change their parameters simultaneously. In this case it is a group of sources, not ROIs. You can click a "channel" from the Source tab and drag it to any element of the Groups list (like copying a file to a folder). It will put this channel/source under this group.
NB: The channel for ROI selection/Measurements is specified in the BigTrace window "Active channel" box. Even if the channel is "not active" in this dialog, BigTrace will use its intensity volume to create/measure ROIs.