EBRAINS - Spatial Anchoring Tools

OBJECTIVES

To register all data from the brain to a common coordinate space.

In coordination with other parts of EBRAINS we have several long-term objectives:

Enable cross modality data analyses to foster new understanding of degenerative diseases using animal models.
Build tools that let scientists easily spatially register their data to a common coordinate space.
Invest in platforms that let scientists share data.
Create metadata models that enable shared data to be semantically mapped into knowledge space.
Build visualisation tools to enable a deeper understanding of registered data.

OFFLINE WORKFLOW

Standalone Tools for Offline Use.

You can complete the entire interactive workflow offline using our standalone software.

The QUINT workflow comprises tools for atlas-registration, feature extraction, for performing spatial analysis and for viewing results.
The tools are designed in collaboration with neuroanatomists.
All our tools are open-source, with publically available GitHub repositories.
Contribute to the project or request new features through our repositories or contact forms.

Atlas Registration

QuickNII

The first step in registering your data is finding the precise plane in the atlas corresponding to your brain section image.

Available both online and offline.
Simplifies complex anatomical analysis.
Save your alignment files for sharing with others.
Partially automated with deep learning using the DeepSlice neural network.

Non-linear adjustments

Visualign

Since slide mounted sections often contain small deformations the initial fit to the atlas will not be perfect. This is why we built Visualign, which allows non-linear refinement of the atlas-registration.

Apply adjustments manually in a simple user interface.
Supports both rat and mouse atlases.
Available both online and offline.

Feature Extraction

ilastik

You will need to extract your features-of-interest from the images using a tool such as ilastik, then you are ready to transform your data into atlas space.

Tool for interactive image classification, segmentation and analysis using supervised machine learning.
Interactively train your classifier to recognise your feature-of-interest, e.g. cells, receptors or markers of pathology.
Export segmentations for use in Nutil.
Available both online and offline.

Spatial analysis

Nutil

Once you have registered your section images to the atlas and segmented the features to be quantified, you are ready to transform your data into atlas space using Nutil.

Contains many utilities for image file preprocessing.
Analyse your data with respect to atlas brain regions.
Generate detailed reports, plot charts and point clouds.
Available both online and offline.

Visualisation

Meshview

Meshview allows you to display point clouds in 3D atlas space.

Orbiting view with toggleable opaque/transparent/hidden atlas parcellation meshes.
Rendering of cut surfaces of the atlas.
Rendering of point clouds.
Compatible with point clouds from the Nutil software.