Polar basecalling - #208
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Implements a parameter-free polar decoder separating amplitude (R, dark-base
detection) from direction (angle theta, base identity).
Two strategies, chosen from encoding matrix E (no chemistry-specific if/else
on channel count):
Orthogonal E (4-ch identity, 3-ch dark-base): argmax(d . E_bright.T)
Non-orthogonal E (2-col Illumina, A fires both channels):
atan2-based angular classification with xtalk-inferred thresholds
Angle thresholds derived parameter-free from the xtalk correction matrix
via _polar_thresholds_from_wcor (midpoints between E_soft centroids).
Results matching polar_basecalling.ipynb:
4-ch Exp C: mapping_rate ~79.4% cells ~74.7% (2,966 watershed cells)
3-ch NIS-seq: mapping_rate ~43.5% nuclei ~85% (1,001 CellPose nuclei)
2-col NIS-seq: mapping_rate ~29.4% nuclei ~84% (superior cell coverage vs SE)
Test data added to scallops/tests/data/:
experimentC/cells.npy watershed cell mask (1024x1024)
nis_seq/ pre-processed NIS-seq HeLa tile40
spots_3ch_corrected.npy (17520, 14, 3) xtalk-corrected 3-ch spots
spots_2col_corrected.npy (17520, 14, 2) synthesised 2-col channels
w_cor_3ch.npy (3, 3) xtalk correction matrix
peaks/labels/nuclei.npy spot metadata and segmentation
barcodes_whitelist.npy 154,646 RC Brunello barcodes
secondary_thr.npy per-chemistry secondary peak thresholds
…for SE (polar was already independent)
…ar-basecalling
…ar-basecalling
…ar-basecalling
…ar-basecalling
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Adding options for sign encoding and polar basecalling methods