diff --git a/.gitbook/assets/image (3).png b/.gitbook/assets/image (3).png new file mode 100644 index 0000000..ef96bc1 Binary files /dev/null and b/.gitbook/assets/image (3).png differ diff --git a/.gitbook/assets/image (4).png b/.gitbook/assets/image (4).png new file mode 100644 index 0000000..8091546 Binary files /dev/null and b/.gitbook/assets/image (4).png differ diff --git a/.gitbook/assets/image (5).png b/.gitbook/assets/image (5).png new file mode 100644 index 0000000..ef96bc1 Binary files /dev/null and b/.gitbook/assets/image (5).png differ diff --git a/.gitbook/assets/image (6).png b/.gitbook/assets/image (6).png new file mode 100644 index 0000000..ef96bc1 Binary files /dev/null and b/.gitbook/assets/image (6).png differ diff --git a/.gitbook/assets/image (7).png b/.gitbook/assets/image (7).png new file mode 100644 index 0000000..8091546 Binary files /dev/null and b/.gitbook/assets/image (7).png differ diff --git a/SUMMARY.md b/SUMMARY.md index 5de4b76..6b59c08 100644 --- a/SUMMARY.md +++ b/SUMMARY.md @@ -14,6 +14,7 @@ * [Working with cameras](usage/scene-1/working-with-cameras.md) * [Using Notebooks](usage/using-notebooks.md) * [Videos, animations and exporting to html](usage/videos-animations-and-exporting-to-html.md) +* [Brainrender GUI](usage/brainrender-gui.md) ## Info diff --git a/usage/brainrender-gui.md b/usage/brainrender-gui.md new file mode 100644 index 0000000..cfba788 --- /dev/null +++ b/usage/brainrender-gui.md @@ -0,0 +1,80 @@ +# Brainrender GUI + +Brainrender now comes with a GUI \(graphical user interface\) for accessing brainrender's functionality without need for writing custom python code. + +{% hint style="info" %} +Currently `bg-brainrender-gui` only supports some of `brainrender`'s core functionality, but we are happy to extend `bg-brainrender-gui` should there be interest in this. +{% endhint %} + +The source code for `bg-brainrender-GUI` can be found at [Github repository](https://github.com/brainglobe/bg-brainrender-gui) where you can also open issues to ask questions or report bugs. + +### Usage + +You can **start** `brainrender-gui` directly from your terminal with the command + +```text +brainrender-gui +``` + +Once the GUI is started it will open a window visualizing the `root` mesh of the atlas selected and several buttons to add and remove elements to the `brainrender` scene. + +![](../.gitbook/assets/image%20%286%29.png) + +{% hint style="success" %} +To s**pecify which atlas to use:** use the **`-a`** argument when calling `brainrender-gui`: + +```text +brainrender-gui -a allen_human_500um # the GUI will use the human atlas +``` +{% endhint %} + +### Adding actors + +The first set of buttons is used to add elements to the `brainrender` scene: + +* `Add brain regions`: clicking on this button opens a new window where you can input the names of the brain regions to be added to the brainrender scene. +* `Add cells`: clicking on this button opens a dialog to select and load a file containing cell coordinates data \(e.g. a `csv` file\). +* `Add from file`: clicking on this button opens a dialog to select and load a file for a 3d mesh \(e.g. a `.obj` file\). + +### Editing actors + +Whenever an actor is added to the scene, its name will be added to the `Actors` list. The list can also be used to edit rendered actors: + +* Double clicking an actor's name **will toggle the visibility** of the corresponding mesh. +* A single click on an actor's name selects it for **editing** with **the `alpha`** \(transparency\) and **`color`** options below the actors list. Once an actor is selected from the `Actors` list, its color and alpha will appear in the text boxes below. Editing the values in these textboxes change the corresponding actor's properties. + + + +### The hierarchy view + +Pressing the `Show structures tree` button at the bottom right of the window shows a panel with the hierarchy view of brain regions in the selected atlas: ![](screenshots/app2.png) + +![](../.gitbook/assets/image%20%287%29.png) + +The hierarchy view can be used to explore the structures hierarchy as well as to add brain regions to the scene: clicking on a region's tick box will add it to the list of actors in the scene. Press the same button again to hide the hierarchy view. + + + +### Taking screenshots + +Under the main canvas there is a button that can be used to save a screenshot with the current view of the `brainrender` scene. + +To specify where to save the screenshot, use the `-o` argument when calling `brainrender-gui`: + +```text +brainrender-gui -o path/to/screenshots/folder +``` + + + +### Camera control + +To the right of the screenshots button is a panel of buttons used to set the camera position in the `brainrender Scene:` + +* `Reset` resets the camera to what is defined as default in `brainrender` \(i.e. `brainrender.CAMERA`\). +* `Top` moves the camera so that the brain is viewed from the top +* `Side1` and `Side2` move the camera to view the brain from the side \(left and right sides\). +* `Front` moves the camera to view the brain from the front. + + +