Multiscale Analysis for N-dimensional Transcriptome Alignment
Meeting 13/02 Talking Points
- Weighting Scheme
- Matching problem
- Plane Matching → Voxelization → Ransac → Umeya/Kabsch → …
Methods
TODO → 18/02/2025
Fix degeneracy in rigid alignment
- Probably due to sparse voxels and spurious couplings?
3D test cases for rigid alignment
3D tilt
3D widespread rotation
Full 3D mouse brain (even/odd)
Download STARmap Data and perform equal registration tasks as with MERFISH
Define axis → Currently model allows to “slice” through planes
- See meeting 13/02
Start working on non-rigid -dimensional registration
Do spatial embeddings improve features?
- Test Novae embedding
- Start working on region-based non-rigid alignment. ⚠️ region-based rigid alignment is probably overkill!
Thesis Parts
- Existing registration methods
- Introduction
- Benchmark
TODO → 13/02/2025
Expand 2D-based RANSAC + Kabsch-Umeyama to 3D
- Does rotation matrix in 3D hold up? ⇒ YES
- Do we need to resort to quaternions? ⇒ YES
Proper error computation
Fix iterative refinement
Optimalization
GIF of alignment
Voxel-match plotting
Determinism in algorithm
Restart (→ prevent local minima in parameter space)
Start working on/discussing the non-rigid alignment
TODO → 06/02/2025
Find voxel correlation algorithm
- Find where voxels should be rigidly aligned to. Some ideas;
- Best correlator (can not handle sparse voxelization!)
- Weighted average of k-best correlators
- Move voxel rigidly towards the found position
- Define maximal neighbourhood depending on voxelization scale (probably one-neighbours ⇒ 27 voxels to check)
TODO → 30/01/2025
Voxelization
- New AnnData object
- Keep center transform in metadata
- Assign cells to voxels (keep in metadata)
- Find good resolution range ⇒ not powers of two, voxels too big in this case!
Mouse Brain Segmentation
- Segment Mouse Brain into 2 datasets (→ Make 3D reconstruction of 200µm slices, 68 slices per dataset)
- Try interpolation in z-axis
- Linear interpolation
- SpatialZ
Manuscript
- Start creating custom Legrand-inspired template
- Make sure to have
- list of tables
- list of figures
- list of abbreviations
- custom TOC
- custom headers (chapter-wise) → full header?
- custom headers (section-wise) → number on side
- custom part indicator (no TOC, overdone!)
- use CMU-bright
- proper BibTex
- Port existing manuscript over