@@ -9,12 +9,22 @@ Any views in `siibra-explorer` can be shared via their URLs. You can use any nat
## Creating short URLs ("saneURL")
Whilst sharing views with URLs are convenient, full URLs are lengthy, fail to be recitable or memorable. While you can use any URL shortener, `siibra-explorer` provide a URL shortener. To access this service, expand navigation panel, click share icon and click `Create custom URL`.
Whilst `siibra-explorer` encodes the current view directly in the URL, such full URLs are quite long and not easily recitable or memorable. You can create short URLs for the current view directly in `siibra-explorer`. To do so,
1. expand the *navigation panel*,
2. click the "share icon", then
3. select `Create custom URL`.
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!!! warning
Links generated by unauthenticated users will expire automatically after 72 hours. To circumvent the expiry, ensure you are logged in using an ebrains user account. Links generated by an authenticated user does not expire.
## Taking Screenshots
Whilst you can use any browser level or OS level screenshot tool, `siibra-explorer` also offers a dedicated screenshot tool which generates a clean and exact image of the current 3D view which automatically hides other user interface elements. To access the screenshot tool, click `Plugin`, then select `Screenshot`.
While you can use any screenshot tool provided by your browser or operating system, `siibra-explorer` offers a dedicated screenshot function which generates a clean image of the current 3D view which hides other user interface elements. To access the screenshot tool,
1. choose the tool menu (`᎒᎒᎒`) from the top right (see [main UI elements](../ui/main_elements.md#tools-and-plugins)), then
2. select `Screenshot`.
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@@ -8,11 +8,11 @@ A typical brain atlas consists of
siibra extends this basic concept by linking multiple spaces and parcellation maps with complementary properties, and combining them with multimodal data features that capture characteristic aspects of brain organisation for locations in the brain.
**Labelled maps vs probability maps.**
## Labelled maps vs probability maps
The above describes what siibra calls a "labelled map", where each location in the brain is uniquely labelled to belong to exactly one brain region. However, siibra also supports "statistical maps", where each location in the brain is mapped to multiple brain regions with different weights (or probabilities). Each coordinate is then not mapped to a single label, but to a vector of weights, one per brain region. The weights for a specific brain region across all coordinates in the brain then form the statistical (or probabilistic) map for this single region, and the statistical maps of multiple regions may overlap.# Datasets linked to locations in the brain
**Multiple reference spaces.**
## Multiple reference spaces
siibra supports different parcellation maps for a given reference space, but also different reference coordinate spaces for a given species. The human brain atlas in EBRAINS provides parcellation maps in
- the MNI 152 space[^1], which is defined by a multi-subject average of structural MRI scans defined at a resolution of about 1mm,
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@@ -21,10 +21,10 @@ siibra supports different parcellation maps for a given reference space, but als
siibra-explorer is designed visualize any of these different types efficiently, by allowing to zoom into very high resolution images, and by offering both volumetric and surface-based viewing modes.
**Relationships between spaces.**
## Relationships between spaces
Some parcellations maps, especially the Julich-Brain cytoarchitectonic maps[^4], are available in all those spaces, this way providing a natural link across those spaces and different spatial scales. An additional link is available through spatial transformations[^5], which map coordinates in one space to their most likely corresponding coordinate in another. These spatial transformations are used by siibra-explorer when you change the reference space, in order to preserve the currently viewed region of interest.
**Datasets linked to locations in the brain.**
## Datasets linked to locations in the brain
siibra provides access to data features anchored to locations in the brain. Locations can be defined in very different ways, such as by specification of a brain region (thus only providing a semantic definition), a coordinate in a reference space, or a bounding box in a reference space. Data features represent datasets hosted on a public repository, typically but not exclusively the EBRAINS Knowledge Graph. A growing share of linked datasets are directly interpreted by siibra-explorer, which means that siibra-explorer offers direct access to the underlying data: Further than just displaying information about the dataset, siibra can visualize the data itself and allows to download it. These directly interpreted features are categorized into molecular, cellular, functional, fibres, connectivity and macrostructural. Many additional datasets are linked to brain regions, which only provide a metadata description and link to the corresponding dataset page on their original repository.
**3D view.** At its core, the viewer presents a 3D view of a brain.
## 3D view
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.
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.
**Navigation panel.** At the top left of the user interface, `siibra-explorer` displays the 3D coordinate of the currently selected center of view. 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)).
## Navigation panel
At the top left of the user interface, `siibra-explorer` displays the 3D coordinate of the currently selected center of view. 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)).
**Parcellation map selectors.** At the bottom of the window, you find buttons to switch between different species, different reference templates, and different parcellation maps (see ["Exploring parcellation maps"](../basics/exploring_3d_parcellation_maps.md)). Note that buttons may be hidden in case that only one option is available.
At the top right of the viewer, there are several icons guiding you to additional functionalites.
- The help button. Here you find information about keyboard shortcuts and terms of use. You can also launch the interactive quick tour, which is launched automatically when you use `siibra-explorer` for the first time.
- The download button, which will download the reference template and parcellation map currently displayed in the viewer
- The plugin menu, which allows you to launch interactive plugins (see “Advanced functionalities”)
- The login menu, which allows you to login with an EBRAINS account to access some custom functionalities for sharing.
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
The download button (<u>↓</u>) will retrieve the reference template and parcellation map currently displayed in a zip file package
### ᎒᎒᎒ 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
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>
