Experiments
This page documents representative experiments reproduced using the packaged RAFT-UP implementation.
Details of every experiment are reported in https://github.com/L1feiyu/raftup_repo/tree/main/examples.
Full slice alignment (Adjacent DLPFC slices)
Setting
Dataset: DLPFC 151509 - DLPFC 151510
Distance between slices: 10 μm
Layer-wise accuracy: 89.3%
Full slice alignment (Far-apart DLPFC slices)
Setting
Dataset: DLPFC 151508 - DLPFC 151509
Distance between slices: 300 μm
Layer-wise accuracy: 86.7%
Full slice alignment (Adjacent MERFISH slices)
Setting
Dataset: MERFISH -0.04 - MERFISH -0.09
Distance between slices: 50 μm
Layer-wise accuracy: 77.7%
Full slice alignment (Far-apart MERFISH slices)
Setting
Dataset: MERFISH -0.04 - MERFISH -0.19
Distance between slices: 150 μm
Layer-wise accuracy: 74.8%
Overlapping-window alignment (synthetic regular window)
Setting
Dataset: DLPFC 151675 window - DLPFC 151675 window
Window type: overlapping regular window
Layer-wise accuracy: 100% and number of aligned spots consistent with ground truth
Overlapping-window alignment (synthetic irregular window)
Setting
Dataset: DLPFC 151675 window - DLPFC 151675 window
Window type: overlapping irregular window
Layer-wise accuracy: 100% and number of aligned spots consistent with ground truth
Spatiotemporal trajectories across developmental stages
Setting
Dataset: Stereo-seq mouse midbrain from E12.5 to E14.5 and from E14.5 to E16.5. Cells are colored by the expert annotations from original study: RGC, radial glia cell; GlioB, glioblast; NeuB, neu- roblast
Spatially preserving analysis of cell-cell communication across slices
Setting
COMMOT(https://commot.readthedocs.io/en/latest/) is applied independently to each slice to infer cell-cell communication (CCC). CCC inferred on slice A is transferred to slice B using the RAFT-UP spot-to-spot mapping, enabling direct comparison to CCC inferred on slice B, and vice versa