Skip to content
Snippets Groups Projects
Commit ab8a9139 authored by Timo Dickscheid's avatar Timo Dickscheid
Browse files

improve ui and quick tour sections

parent 08e92009
No related branches found
No related tags found
No related merge requests found
# Launch & quick start
To launch siibra-explorer on EBRAINS, go to **<https://atlases.ebrains.eu/viewer>** using your web browser.
!!! note
To launch siibra-explorer on EBRAINS, point your webbrowser to:
**<https://atlases.ebrains.eu/viewer>**
Recommended browsers are up-to-date versions of [Firefox](https://www.mozilla.org/firefox) and [Google chrome](https://www.google.com/chrome). Newer versions of [Apple Safari](https://www.apple.com/safari/) also work fairly well. Note that your hardware needs to support the WebGL2 standard, which should be the case for recent devices. If in doubt, check compatibility at <https://get.webgl.org/webgl2/>.
!!! tip "siibra-explorer runs on mobile devices!"
......
......@@ -4,30 +4,27 @@
At its core, the viewer presents a 3D view of a brain.
The precise layout of the 3D view depends on the select reference space.
For volumetric reference spaces, it presents 2D views of three orthogonal planes in the reference template, combined with a rotatable 3D overview of the brain surface indicating the location of these planes. The planes default to the coronal, sagittal and axial plane, and can be freely adjusted in position and orientation to select arbitrary oblique views.
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-waxholm.png){: style="width:250px" }
The volumetric views support ultrahigh-resolution data, and can be zoomed in if the underlying image data allows. Each of the 3 planar views can be maximized using the "[ ]" icon in each view.
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-waxholm.png){: style="width:300px" }
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-v1border.png){: style="width:250px" }
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-surfaceview.png){: style="width:235px" }
For pure surface spaces, such as the fsaverage space, the viewer shows only a 3D view.
- (Left) For volumetric reference spaces, it presents 2D views of three orthogonal planes in the reference template, combined with a rotatable 3D overview of the brain surface indicating the location of these planes. The planes default to the coronal, sagittal and axial plane, and can be freely adjusted in position and orientation to select arbitrary oblique views.
- (Middle) The volumetric views support ultrahigh-resolution data, and can be zoomed in if the underlying image data allows. Each of the 3 planar views can be maximized using the "[ ]" icon in each view.
- (Right) For pure surface spaces, such as the fsaverage space, the viewer shows only a 3D view.
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-surfaceview.png){: style="width:250px" }
## Navigation panel 🧭
## Navigation panel
At the top left of the user interface, `siibra-explorer` displays the 3D coordinate of the currently selected center of view together with the navigation icon 🧭. When you click it with the mouse pointer, a navigation panel opens, which allows to enter a different coordinates, and create a shareable link to the current view (see ["Storing and sharing 3D views"](../basics/storing_and_sharing_3d_views.md)).
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-navigation.png){ style="width:600px"}
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-navigation.png){ style="width:500px"}
## Parcellation map selectors
At the bottom of the window, you find buttons to switch between different species, different reference templates, and different parcellation maps.
Working with different maps is described in ["Exploring parcellation maps"](../basics/exploring_3d_parcellation_maps.md)).
Note that some of the buttons may be hidden in case that only one option is available.
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-chips.png){ style="width:600px"}
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-chips.png){ style="width:500px"}
## Tools and plugins
......@@ -35,34 +32,18 @@ At the top right of the viewer, there are several icons guiding you to additiona
![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-tools.png){ style="width:500px"}
### ⓘ Help panel
#### ⓘ Help panel
The help button (ⓘ ) opens information about keyboard shortcuts and terms of use. Here you can also launch the interactive quick tour, which is started automatically when you use `siibra-explorer` for the first time.
### <u>↓</u> Download current view
#### <u>↓</u> Download current view
The download button (<u></u>) will retrieve the reference template and parcellation map currently displayed in a zip file package
### ᎒᎒᎒ Plugins
#### ᎒᎒᎒ Plugins
The plugin button (᎒᎒᎒) reveals a menu of interactive plugins, including advanced tools for [annotation](../advanced/annotating_structures.md) and [differential gene expression analysis](../advanced/differential_gene_expression_analysis.md)
### 👤 Sign in with EBRAINS
#### 👤 Sign in with EBRAINS
The login button (👤) allows you to sign in with an EBRAINS account to access some custom functionalities for sharing.
!!! tip "Get an EBRAINS account!"
You can sign up for a free EBRAINS account at <https://ebrains.eu/register>
| Action | Desktop | Touch devices |
| --- | --- | --- |
| Translate / Pan | `[drag]` any of the slice views | `[drag]` any of the slice views |
| Oblique rotation | `<shift>` + `[drag]` any of the slice views | `[rotate]` any of the slice views |
| Zoom | `[mousewheel]` | `[pinch zoom]` |
| Zoom | `[hover]` on any slice views > `[click]` magnifier | `[tap]` on magnifier |
| Next slice | `<ctrl>` + `[mousewheel]` / `[p]`revious / `[n]`ext | - |
| Next 10 slice | `<shift>` + `[mousewheel]` | - |
| Toggle delineation | `[q]` | - |
| Toggle cross hair | `[a]` | - |
| Multiple region select | `<ctrl>` + `[click]` on region | - |
| Context menu | `[right click]` | - |
You can enable touch interface by `[Portrait]` > `Settings` > `Enable Mobile UI`
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment