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name: tile-snake-pattern-stitching description: "SNAKE vs RASTER tile acquisition patterns for image stitching in KINTSUGI" author: KINTSUGI Team date: 2024-12-15

Tile SNAKE Pattern Stitching - Research Notes

Experiment Overview

Context

CODEX and similar multiplex imaging systems acquire tiles in a SNAKE pattern (also called serpentine or boustrophedon). This pattern alternates direction on each row to minimize stage movement. Incorrect tile ordering causes stitching failures with misaligned or scrambled images.

SNAKE vs RASTER Pattern

SNAKE Pattern (Default for CODEX)

Even rows scan left-to-right, odd rows scan right-to-left:

CopyRow 0:  →  →  →  (tiles 1, 2, 3)
Row 1:  ←  ←  ←  (tiles 6, 5, 4)
Row 2:  →  →  →  (tiles 7, 8, 9)

RASTER Pattern

All rows scan left-to-right:

CopyRow 0:  →  →  →  (tiles 1, 2, 3)
Row 1:  →  →  →  (tiles 4, 5, 6)
Row 2:  →  →  →  (tiles 7, 8, 9)

Verified Workflow

Building Tile Coordinates for SNAKE Pattern

Copyfrom itertools import chain, repeat

n_rows = 2  # Grid rows
n_cols = 2  # Grid columns

# Row indices (same for both patterns)
rows = list(chain.from_iterable(repeat(row, n_cols) for row in range(n_rows)))

# Column indices - SNAKE PATTERN
# Even rows: 0,1,2... (L→R)
# Odd rows: ...2,1,0 (R→L)
cols = list(chain.from_iterable(
    range(n_cols) if row % 2 == 0 else range(n_cols - 1, -1, -1)
    for row in range(n_rows)
))

# For 2x2 grid:
# rows = [0, 0, 1, 1]
# cols = [0, 1, 1, 0]  <- SNAKE: second row reversed

Test Data Tile Reordering

When test data tiles are renamed by POSITION (1,2,3,4 for grid positions) but were acquired in SNAKE order, reorder before stitching:

Copy# Files load as position order: [tile1, tile2, tile3, tile4]
# Grid positions:
#   [1] [2]    row 0 (L→R)
#   [3] [4]    row 1 (should be R→L for snake)
#
# For snake acquisition, row 1 was acquired as [4, 3] not [3, 4]
# So actual acquisition order was: 1, 2, 4, 3
#
# Reorder to match acquisition order:
if n_rows == 2 and n_cols == 2:
    corrected = corrected[[0, 1, 3, 2]]  # [1,2,3,4] → [1,2,4,3]

Failed Attempts (Critical)

Final Parameters

SNAKE Pattern Coordinates (2x2 grid)

Copyrows = [0, 0, 1, 1]
cols = [0, 1, 1, 0]  # NOT [0, 1, 0, 1] (that's RASTER)

SNAKE Pattern Coordinates (3x3 grid)

Copyrows = [0, 0, 0, 1, 1, 1, 2, 2, 2]
cols = [0, 1, 2, 2, 1, 0, 0, 1, 2]  # Row 1 reversed

General Formula

Copycols = list(chain.from_iterable(
    range(n_cols) if row % 2 == 0 else range(n_cols - 1, -1, -1)
    for row in range(n_rows)
))

Key Insights

• SNAKE pattern is standard for CODEX and similar multiplex imaging systems
• The pattern minimizes stage travel time between tiles
• Even rows: left-to-right (columns 0,1,2...)
• Odd rows: right-to-left (columns ...2,1,0)
• When test data tiles are renamed by position, they must be reordered to match acquisition order before stitching
• The stitch model is computed from tile positions, so tile array order must match the coordinate lists

References

• CODEX multiplex imaging documentation
• KINTSUGI Notebook 1 (Single Channel Eval) and Notebook 2 (Cycle Processing)