Timo Dickscheid

Validate region trees to be strict DAGs on construction

2

Some region trees seem to have inconsistent definitions and lead to regions containing themselves as a child region. This must not happen and needs to be fixed, and validated on...

Provide access to surface meshes for different parcellations

4

The meshes are currently maintained as neuroglancer mesh format on atlas VMs. The library needs to be able to forard the site URL, read them and also convert them to...

- [x] Write a feature query to connect to their API - [ ] Connect their region definitions with the Julich-Brain parcellation - [ ] implement morphology feature type

Currently, regional data features are only found if the parcellation matches the associated region specification. It would be good to allow approximate links, so that features are also found by...

https://github.com/brainets/frites

Building mask from Julich parent node fails

1

Observed in version 1.0a14: ```python import siibra p = siibra.parcellations.get('julich 3') isocortex = p.get_region('cerebral cortex') isocortex.get_regional_map(space='mni152', maptype='labelled') ``` fails when it ends up trying to merge less than two volumes...

siibra python 1.0a14 triggers downstream problems when querying gene expressions with empty response. siibra will then generate an empty gene expression features, with an empty point list as location, which...

Proper handling of VOI specifications when fetching across neuroglancer fragment volumes

1

When fetching from a multi-fragment neuroglancer provider with a voi, the current implementation returned a full-size but almost empty volume. This PR tries to fix the problem, and had to...

[ENH] Add 2015 reconstruction of BigBrain as a template coordinate space

2

I propose to add BigBrain as a known template space. This will help us to properly model a couple of incoming EBRAINS datasets in a BIDS conform way.