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Add BVV settings documetation
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ekatrukha committed Dec 18, 2024
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23 changes: 18 additions & 5 deletions tutorials/bigvolumeviewer.md
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## Using BigVolumeViewer

By selecting a **B** checkbox in the Sources panel, you can view the 3D dataset in the BigVolumeViewer (BVV) window.
<img width="400" alt="image" src="./tutorial_images/sources_buttons.png">
<img width="400" alt="image" src="./tutorial_images/bvv/sources_buttons_bvv.png">

BVV navigation controls (rotation, zoom, etc) are [the same as in BigDataViewer](./explore_a_project.html#browsing).

It supports two rendering modes: Maximum Intensity projection and Volumetric (transclucent/alpha blending), see an example below.
You can toggle between them using keyboard shortcut <kbd>O</kbd> (letter, not a number).
You can toggle between them using keyboard shortcut **`O`** (letter, not a number).

<img width="800" alt="comparison of rendering modes, left=max, right=volumetric" src="./tutorial_images/bvv/bvv_render_style.png">

You can synchronize the dataset view (and timepoint) with the BigDataViewer window view using shortcut <kbd>D</kbd>.
You can synchronize the dataset view (and timepoint) with the BigDataViewer window view using shortcut **`D`**.

Compared with 3DViewer volume rendering using a fixed resolution, BVV works directly with the raw data. It loads corresponding multi-resolution data levels depending on the current view.

Expand All @@ -19,13 +19,26 @@ As with all 3D applications, a better GPU card with large amount of GPU memory i

### Adjusting brightness, contrast and opacity

As with BigDataViewer, you can configure the appearance of each source in BVV using shortcut <kbd>S</kbd> (also in the Cards Panel, activated by a shortcut <kbd>P</kbd>).
As with BigDataViewer, you can configure the appearance of each source in BVV using shortcut **`S`** (also in the Cards Panel, activated by a shortcut **`P`**).
Upon loading a source to BVV, its contrast and range will be taken from the current BDV source settings.
The square on the left shows a color that is used to display the volume.
You can change it using left click. Or you can apply Fiji installed LUT using right-click.
<img alt="LUT selection example" src="./tutorial_images/bvv/bvv_lut_selection.gif">
<img width="500" alt="LUT selection example" src="./tutorial_images/bvv/bvv_lut_selection.gif">
The top slider maps minimum and maximum shade of selected source color (or min and max of LUT) to the selected data range (like a standard Fiji's "brightness" dialog).
There are additional source display setting, which you can expand by clicking on "three triangles" bar:
<img width="500" alt="expand settings" src="./tutorial_images/bvv/bvv_expand_brightness.gif">




### BigVolumeViewer settings

To change BVV settings, right click on the BigDataViewer window and select "Configure BigVolumeViewer Rendering".
Short parameters description (and [a bit longer](https://forum.image.sc/t/bigvolumeviewer-tech-demo/12104), if interested) :

- **Render width and height** - the true quality of 3D rendering performed by GPU and stretched to the current window size. Increasing them makes better picture at the expense of higher computational load;
- **Dither window size** and **number of dither samples**. Interpolating nearby pixels (withing the window) instead of sampling the volume. Increasing these values will speed up rendering at the expense of quality;
- **GPU cache tile size** size of the 3D blocks (in pixels) that are loaded to GPU;
- **GPU cache size (in MB)** limits the storage of the data in GPU memory. Increasing this parameter speeds up data display (should be less then your GPU memory).
- **Camera distance**, **Clip distance far/near** parameters define [viewing frustum](https://en.wikipedia.org/wiki/Viewing_frustum) of the perspective virtual camera. See a picture below to get an idea. "Camera distance" should be always larger than "clip distance near". If you want to get "BDV slice" view, you can set "clip distance near" to zero.
<img width="600" alt="comparison of rendering modes, left=max, right=volumetric" src="./tutorial_images/bvv/bvv_frustum.png">
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