📝 Event: 2026-11-21_repeatability_warning

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📊 Report Overview

Event Metadata

Record Type
Qc Session

Reason / Suite
Troubleshooting

Operator
Ida Laine

Instrument
scope-testx1

QC Summary & Evaluation

Summary: QC before service captured intermittent stage position loss after long screening simulations.

WARN

psf.60x_oil.525.fwhm_z_nm: Stage repeatability exceeded warning limit, suggesting encoder path issue.

🔬 Tests Performed

Test Type	Details
Laser Power	Linearity and 20-minute stability check at objective plane.
Psf	175 nm bead stack in 488 channel.
Alignment	Multicolor bead co-registration check (488/561).
Stage	Stage repeatability assay over 100 cycles.

📏 Computed Metrics

Metric ID	Value
`laser.488.linearity_r2`	0.997
`psf.60x_oil.525.fwhm_xy_max_nm`	240
`psf.60x_oil.525.fwhm_xy_min_nm`	240
`psf.60x_oil.525.fwhm_z_nm`	620
`chromatic_shift.60x_oil.561_to_488.dist_nm`	70
`stage.repeatability_sigma_x_nm`	360
`stage.repeatability_sigma_y_nm`	310

📎 Artifacts & References

Artifact ID	Role	Description
`art_laser_linearity_csv`	TABLE	Laser setpoint sweep.: `omero://aic-core/scope-testx1/2026/dataset/qc_scope-testx1_20261121T1700Z_repeatability_v1/laser_linearity.csv`
`art_laser_stability_csv`	TABLE	Laser stability time series.: `omero://aic-core/scope-testx1/2026/dataset/qc_scope-testx1_20261121T1700Z_repeatability_v1/laser_stability.csv`
`art_psf_stack_raw`	RAW_IMAGE	PSF bead stack.: `omero://aic-core/scope-testx1/2026/image/qc_scope-testx1_20261121T1700Z_repeatability_v1_psf`
`art_psf_preview`	PREVIEW	PSF MIP preview.: `qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20261121T1700Z_repeatability_v1_psf_mip.png`
`art_coreg_stack_raw`	RAW_IMAGE	Co-registration stack.: `omero://aic-core/scope-testx1/2026/image/qc_scope-testx1_20261121T1700Z_repeatability_v1_coreg`
`art_coreg_preview`	PREVIEW	Co-registration overlay preview.: `qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20261121T1700Z_repeatability_v1_coreg_overlay.png`
`art_stage_repeat_raw`	RAW_IMAGE	Stage repeatability acquisition.: `omero://aic-core/scope-testx1/2026/image/qc_scope-testx1_20261121T1700Z_repeatability_v1_stage`
`art_stage_repeat_plot`	PREVIEW	Stage repeatability plot.: `qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20261121T1700Z_repeatability_v1_stage_repeat.png`

Additional Notes

Repeatability variance increased late in 500-cycle run; symptoms matched overnight plate abort reports.

📄 Raw YAML Ledger

View 2026-11-21_repeatability_warning.yaml

schema_version: 1
record_type: qc_session
qc_id: qc_scope-testx1_20261121T1700Z_repeatability_v1
microscope: scope-testx1
started_utc: '2026-11-21T17:00:00Z'
ended_utc: '2026-11-21T17:50:00Z'
reason: troubleshooting
summary: QC before service captured intermittent stage position loss after long screening
  simulations.
notes: 'Repeatability variance increased late in 500-cycle run; symptoms matched overnight
  plate abort reports.

  '
performed:
- qc_type: laser_power
  details: Linearity and 20-minute stability check at objective plane.
  artifacts:
  - art_laser_linearity_csv
  - art_laser_stability_csv
- qc_type: psf
  details: 175 nm bead stack in 488 channel.
  artifacts:
  - art_psf_stack_raw
  - art_psf_preview
- qc_type: alignment
  details: Multicolor bead co-registration check (488/561).
  artifacts:
  - art_coreg_stack_raw
  - art_coreg_preview
- qc_type: stage
  details: Stage repeatability assay over 100 cycles.
  artifacts:
  - art_stage_repeat_raw
  - art_stage_repeat_plot
inputs_human:
- metric_id: visual.optics_clean
  value: 'yes'
  unit: ''
  details: No visible residue on objective front lens.
  metric_class: signal_to_noise
laser_inputs_human:
  measurement_position: at_objective
  measurement_position_details: 60x/1.4 objective with calibrated photodiode adapter.
  power_meter:
    model: Thorlabs PM100D + S170C
    serial: PMD-AX41-228
    calibration_due: '2026-12-31'
    integration_time_s: 1.0
    notes: Room temp 22 C, humidity 41%.
  linearity_series:
  - laser: '488'
    setpoint_units: percent
    power_units: mW
    points:
    - setpoint: 10
      power: 0.22
    - setpoint: 20
      power: 0.44
    - setpoint: 50
      power: 1.1
    - setpoint: 100
      power: 2.17
    csv_artifact: art_laser_linearity_csv
    details: Single sweep after 10-minute warm-up.
  stability_series:
  - laser: '488'
    setpoint: 80
    setpoint_units: percent
    sampling: 1 Hz for 5 min
    power_units: mW
    timepoints:
    - t_s: 0
      power: 1.75
    - t_s: 120
      power: 1.74
    - t_s: 300
      power: 1.75
    details: Short-term stability check for trend continuity.
computed_provenance:
  pipeline: aic_qc_pipeline
  version: 1.4.0
  git_commit: 7c4a9d1
  run_utc: '2026-11-21T17:50:00Z'
metrics_computed:
- metric_id: laser.488.linearity_r2
  value: 0.997
  unit: unitless
  metric_class: laser_power
- metric_id: psf.60x_oil.525.fwhm_xy_max_nm
  value: 240
  unit: nm
  metric_class: fwhm_lateral
- metric_id: psf.60x_oil.525.fwhm_xy_min_nm
  value: 240
  unit: nm
  metric_class: fwhm_lateral
- metric_id: psf.60x_oil.525.fwhm_z_nm
  value: 620
  unit: nm
  metric_class: fwhm_axial
- metric_id: chromatic_shift.60x_oil.561_to_488.dist_nm
  value: 70
  unit: nm
  metric_class: chromatic_shift
- metric_id: stage.repeatability_sigma_x_nm
  value: 360
  unit: nm
  metric_class: stage_repeatability
- metric_id: stage.repeatability_sigma_y_nm
  value: 310
  unit: nm
  metric_class: stage_repeatability
evaluation:
  benchmark_ref: benchmarks/scope-testx1.yaml@main
  evaluated_utc: '2026-11-21T17:50:00Z'
  evaluated_by: github_action:qceval
  overall_status: warn
  results:
  - metric_id: psf.60x_oil.525.fwhm_z_nm
    status: warn
    threshold: warn>600nm, fail>750nm
    message: Stage repeatability exceeded warning limit, suggesting encoder path issue.
artifacts:
- artifact_id: art_laser_linearity_csv
  role: table
  uri: omero://aic-core/scope-testx1/2026/dataset/qc_scope-testx1_20261121T1700Z_repeatability_v1/laser_linearity.csv
  description: Laser setpoint sweep.
- artifact_id: art_laser_stability_csv
  role: table
  uri: omero://aic-core/scope-testx1/2026/dataset/qc_scope-testx1_20261121T1700Z_repeatability_v1/laser_stability.csv
  description: Laser stability time series.
- artifact_id: art_psf_stack_raw
  role: raw_image
  uri: omero://aic-core/scope-testx1/2026/image/qc_scope-testx1_20261121T1700Z_repeatability_v1_psf
  description: PSF bead stack.
- artifact_id: art_psf_preview
  role: preview
  uri: qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20261121T1700Z_repeatability_v1_psf_mip.png
  description: PSF MIP preview.
- artifact_id: art_coreg_stack_raw
  role: raw_image
  uri: omero://aic-core/scope-testx1/2026/image/qc_scope-testx1_20261121T1700Z_repeatability_v1_coreg
  description: Co-registration stack.
- artifact_id: art_coreg_preview
  role: preview
  uri: qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20261121T1700Z_repeatability_v1_coreg_overlay.png
  description: Co-registration overlay preview.
- artifact_id: art_stage_repeat_raw
  role: raw_image
  uri: omero://aic-core/scope-testx1/2026/image/qc_scope-testx1_20261121T1700Z_repeatability_v1_stage
  description: Stage repeatability acquisition.
- artifact_id: art_stage_repeat_plot
  role: preview
  uri: qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20261121T1700Z_repeatability_v1_stage_repeat.png
  description: Stage repeatability plot.
performed_by: Ida Laine