Next-stage functionalities

vijayiyer05 commented 2 years ago

Will capture further functionalities with referenced Python snippets in this issue

dickscheid commented 2 years ago

This should comprise:

[ ] Download and caching of continuous maps in MNI space for applicable parcellations (Julich-Brain, DiFuMo, Long & short fibre bundles), and efficient assignment of nonzero probabilities to individual coordinates given in MNI space
[ ] Queries and access to neurotransmitter receptor distributions and cell distributinos as tabular and image data (reference snippet 1, reference snippet 2)
[ ] Queries and access to connectivity matrices and regional profiles as tabular data (reference snippet)
[ ] Queries for general EBRAINS datasets with metadata and download links (reference snippet)
[ ] Appropriate and convenient storage of downloaded data to local files outside the cache for reuse (nifti images for 3D images, pngs for 2D images, tsv/xlsx for tabular data)

Each item should be demonstrated using a short, clearly documented live script.

vijayiyer05 commented 1 year ago

@dickscheid Before staring the next project cycle, I think it would be good to capture the status of the punchlist items here & close this out if indicated (any odds & ends could become new issues).

dickscheid commented 1 year ago

We reviewed the above list today, here is an updated status/plan

[x] Queries and access to connectivity matrices
[x] Queries and access to neurotransmitter receptor distributions
[ ] Queries and access to cell distributions as tabular and image data
[ ] include cortical profiles in neurotransmitter distribution features
[ ] proper handling of other parcellations in MNI space (Difumo variants; bundle maps) plus a testing framework for this
[ ] Queries for general EBRAINS datasets with metadata and download links
[ ] Access to neuroglancer image source and regions of interest therein, specified by bounding box, returning lower field of view or lower resolution image as a Nifty image object
[ ] Access to parcellations and templates in surface format (esp. free surfer template and Julich-brain map in freesurfer space)
[ ] call to anatomical assignment backend to decode a coordinate into a set of matching brain regions with probability information

dickscheid commented 5 months ago

Most of these points will become simpler once the toolbox is migrated to siibra-api 3

FZJ-INM1-BDA / siibralab

Next-stage functionalities #7