nanodevice_gdsalign

nanodevice_gdsalign — GDS Template Alignment

Align microscope images to a GDS fabrication template by detecting lithographic markers in both domains and computing a similarity transform.

Coordinate system after gdsalign: Coordinates in traces_gds.json are in the GDS reference frame (floating-point micrometers). When using them in execute_script, convert to dbu via int(value_um / layout.dbu). Do NOT apply the flakedetect_commit image-center transform — gdsalign already handles the coordinate mapping.

Prerequisites

• Conda env instrMCPdev with opencv, numpy, scipy, gdstk
• Template GDS file with L5/0 alignment markers (4 cross pairs)
• flakedetect output: traces.json with material contours in pixel coordinates
• All scripts: ${PYTHON_PATH:-conda run -n instrMCPdev python} <script>

Default Output Directory

If the user does not specify an output path, default to <stack_image_dir>/output/gdsalign/ (the directory containing the source images). Never use /tmp as the default output.

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Agent Workflow

1. extract_markers — Parse GDS, find 4 innermost L5/0 marker pairs
   → gds_markers.json (pair centers + bounding boxes in um)

2. detect_markers — Find marker crosses in microscope image
   → image_markers.json (detected centers in pixel coordinates)

3. align_gds — Match GDS↔image marker pairs, compute reflected similarity
   → gds_warp.npy (2x3 affine), gds_alignment_report.json

4. commit_gds — Warp image + transform contours, commit to KLayout
   → full_stack_gds.png, traces_gds.json, image_placement.json

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Scripts Reference

extract_markers.py

${PYTHON_PATH:-conda run -n instrMCPdev python} skills/nanodevice_gdsalign/scripts/extract_markers.py \
    --gds Template.gds --output-dir output/gdsalign/

Parses GDS, finds all L5/0 polygons, selects the 8 closest to grid center, groups into 4 pairs by proximity, labels NE/NW/SE/SW.

Outputs: gds_markers.json

detect_markers.py

${PYTHON_PATH:-conda run -n instrMCPdev python} skills/nanodevice_gdsalign/scripts/detect_markers.py \
    --image stack.png --pixel-size <um/px> \
    --gds-markers output/gdsalign/gds_markers.json \
    --output-dir output/gdsalign/

Renders marker-pair templates from gds_markers.json, then runs multi-method template matching (grayscale, inverted, CLAHE, edge) with geometric consistency filtering to find the 4 marker pairs.

Outputs: image_markers.json, 01_template.png, 03_detections.png

Verification: After running, view 03_detections.png. The 4 detected markers (colored circles) should form a roughly square pattern, ~300-400 um apart (a few thousand pixels at 0.087 um/px), centered in the image near the flake region. The pixel_size parameter is critical for correct template rendering — use the value specified in the task instructions (typically 0.087 um/px). If detections look wrong (markers on image edges, or only 2-3 found), check that pixel_size matches the actual microscope magnification.

align_gds.py

${PYTHON_PATH:-conda run -n instrMCPdev python} skills/nanodevice_gdsalign/scripts/align_gds.py \
    --gds-markers output/gdsalign/gds_markers.json \
    --image-markers output/gdsalign/image_markers.json \
    --output-dir output/gdsalign/

Exhaustive enumeration over 2-point correspondences finds the best reflected similarity (image Y-down → GDS Y-up), then least-squares refinement over all inliers. Automatically resolves rotational ambiguity (90°/180°/270°) for symmetric marker patterns by preferring the solution closest to 0° rotation.

Outputs: gds_warp.npy (2×3 affine matrix), gds_alignment_report.json

commit_gds.py

${PYTHON_PATH:-conda run -n instrMCPdev python} skills/nanodevice_gdsalign/scripts/commit_gds.py \
    --warp output/gdsalign/gds_warp.npy \
    --traces output/combine/traces.json \
    --image full_stack_raw.jpg --pixel-size <um/px> \
    --gds Template.gds --output-dir output/gdsalign/ [--warp-only]

Warps the microscope image and material contours into GDS coordinates using the affine from align_gds.py. Without --warp-only, also loads the GDS template into KLayout, adds the warped image as a background overlay, and inserts material polygons on layers 10–13.

Flag	Description
--warp	Path to gds_warp.npy (2×3 affine matrix)
--traces	Path to traces.json from flakedetect (with contour_um fields)
--image	Full-stack microscope image
--pixel-size	Image pixel size in um/px
--gds	Template GDS file (loaded into KLayout during commit)
--output-dir	Optional output directory for warp results (default: current working directory). Set this to the agent's workspace directory to keep warp outputs scoped. Files written: traces_gds.json, full_stack_gds.png, image_placement.json
--warp-only	Only produce warped files, skip KLayout commit
--mcp-config	Path to MCP config JSON. Fallback chain: .mcp.json in CWD → mcp_config.json in project root → default 127.0.0.1:8765. In Docker, pass a config pointing to http://host.docker.internal:8765/mcp
--align-report	Path to gds_alignment_report.json for the registration gate. Default: auto-located next to --warp.
--gds-markers	Path to gds_markers.json for the marker-field frame check. Default: auto-located next to --warp.
--skip-registration-check	Escape hatch — strongly discouraged. Bypasses the registration self-validation gate. Only for an intentional hand-built transform.

Outputs: full_stack_gds.png, traces_gds.json, image_placement.json

⚠️ Validated-commit contract — commit flakes ONLY through commit_gds.py

commit_gds.py is the only sanctioned way to place flake polygons in the GDS frame. Do NOT hand-place flakes via execute_script with a hand-built transform (a centered shift / Y-flip / "1:1 at origin"). That is the dominant failure mode (HM08/QH06/AH06): the device looks perfect against the agent's own flakes but lands hundreds of um off the real marker field and scores ~0.

Before committing, commit_gds.py runs a registration self-validation gate (no ground truth — only the alignment report, the marker grid, and your own warped contours). It hard-fails (exit 3) when:

• there is no gds_alignment_report.json next to the warp (alignment was skipped / hand-rolled),
• the alignment is bad (< 3 inliers or mean residual > 5 um),
• the --warp matrix does not match the alignment report (a stale/hand-built transform), or
• the warped flakes land outside the L5 marker field.

If the gate fails, FIX the alignment — do not bypass it. Almost always the cause is a wrong pixel_size: re-run validate_pixel_size, then detect_markers → align_gds, and commit the resulting gds_warp.npy. Only pass --skip-registration-check if you are deliberately committing a hand-built transform and understand it will likely be off-frame.

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Acceptance Thresholds

Metric	Pass	Fail
Markers detected	>= 3	< 3
Inliers (align_gds)	>= 2	< 2
Mean residual	< 5.0 um	>= 5.0 um

Fail on any metric: Do NOT commit to KLayout. Check diagnostic images and retry.

Known Behaviour

• Rotational ambiguity: Square marker grids have rotational symmetry — θ, θ+90°, θ+180°, θ+270° can yield similar residuals. align_gds.py automatically tries all four companions and picks the one with rotation closest to 0°.
• PNG orientation: The warped PNG (full_stack_gds.png) is vertically flipped on save so that row 0 holds GDS-north data. KLayout's pya.Image renders PNG row 0 at the high-Y edge of the placement bbox, so the image ends up right-side-up when placed at origin_um = (x_min, y_min) with identity rotation. If you inspect the PNG in a file viewer it will already look correct (north at top).
• Image ↔ contour consistency: The warped image and the transformed contours (traces_gds.json) are produced from the same affine. If you re-run the alignment at a different pixel_size, you must also re-run commit_gds.py with the same pixel_size. Mixing a gds_warp.npy produced at one pixel size with commit_gds.py --pixel-size at another will place the image at the wrong scale (the scale factor in the warp matrix compensates for the pixel_size used during alignment).
• Destructive commit: commit_gds.py calls layout.clear() before loading the template into KLayout, so any pre-existing geometry in the current tab is wiped. This is intentional — it avoids cell-name collisions in Layout.read() that otherwise leave orphaned cell indices. Run commit_gds.py against a fresh tab (or use the create_layout MCP tool first) if you have ongoing work you don't want to lose.

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Pixel Size Validation

The pixel_size parameter (um/px) is critical for correct template rendering in detect_markers.py and image placement in commit_gds.py. Always validate the pixel size before running the pipeline.

Common pixel_size values by objective magnification:

Objective	Typical pixel_size (um/px)
100x	0.05
100x (alt)	0.087
50x	0.1
20x	0.25
10x	0.5

Use validate_pixel_size to confirm the value before running the alignment pipeline. If the pixel size is wrong, marker detection will fail or produce incorrect transforms.

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Exit Codes

Code	Meaning
0	Success
1	Error (missing file, insufficient markers, transform failure)
3	commit_gds.py registration self-validation failed (skipped/hand-rolled/off-frame transform) — fix the alignment, do not bypass