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SGE Reorientation (sge_orientate)

Overview

sge_orientate rotates and flips an SGE to match the desired image orientation.

Not part of run_together

run_together does not reorient the SGE; sge_stitch calls sge_orientate for tiles that need it. Use this page to reorient an SGE directly in step-by-step or custom workflows.

Requirements

  • Input SGE in the unified format (from SGE format conversion). The coordinate columns must be named X and Y (fixed; not configurable), and the min/max file must be the two-column xmin/xmax/ymin/ymax TSV.

Actions

Rotations are clockwise; flips are applied after rotation. The SGE is transformed within its own bounding box, so the coordinate range is preserved (with X and Y ranges swapped for 90°/270°).

Example Usage

Below is an example with 90 degree rotation and a horizontal flip.

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OUT_PREFIX=r90_hflip                # Replace r90_hflip with your prefix
cartloader sge_orientate  \
    --in-transcript /path/to/transcripts.unsorted.tsv.gz \
    --in-feature  /path/to/feature.clean.tsv.gz \
    --in-minmax /path/to/coordinate_minmax.tsv \
    --out-transcript /path/to/${OUT_PREFIX}.transcripts.unsorted.tsv.gz \
    --out-feature /path/to/${OUT_PREFIX}.feature.clean.tsv.gz \
    --out-minmax  /path/to/${OUT_PREFIX}.coordinate_minmax.tsv \
    --rotate 90 \
    --flip-horizontal

Parameters

Input/Output Parameters

All six are required.

  • --in-transcript (str): Input transcript SGE TSV (gzipped).
  • --in-feature (str): Input feature TSV (gzipped).
  • --in-minmax (str): Input coordinate min/max TSV.
  • --out-transcript (str): Output oriented transcript SGE TSV (gzipped).
  • --out-feature (str): Output feature TSV (an unchanged copy of the input).
  • --out-minmax (str): Output oriented min/max TSV.

Key Parameters

  • --rotate (90|180|270): Rotate clockwise (applied before flips). Omit for no rotation.
  • --flip-vertical (flag): Flip vertically (along the Y-axis; applied after rotation).
  • --flip-horizontal (flag): Flip horizontally (along the X-axis; applied after rotation).
  • --chunk-size (int): Rows per chunk when processing the transcript TSV (default: 1,000,000).

Equivalent combinations are normalized first (e.g. --rotate 180 is the same as both flips).

Output

The oriented transcript TSV and min/max TSV, plus a copy of the feature TSV, at the three --out-* paths.