Back to Neuroinformatics Unit
GSoC 2026

brainglobe-cellfinder: expand input support to 2.5D and single-channel data (Soumya Snigdha Kundu)

Cellfinder currently expects full 3D whole-brain volumes with both signal and background channels, so brain slices (2.5D) and single-channel acquisitions are not first-class citizens. The codebase also mixes axis conventions, which makes dimensionality changes error-prone. A recent data-loading refactor introduces explicit axis tracking and a new class hierarchy for cube generation and augmentation; the 2D/2.5D and single-channel work proposed here will build on that foundation. The core deliverables are to standardise axis semantics as the foundation, add a 2D detection path for brain slices and refactor classification to support both 2D and 3D inputs, and make the background channel optional across the main API and classification pipeline.

Project details

Contributor

Soumya Snigdha Kundu

Mentors

Not available

Technologies

Not listed in the archive