📝 Event: 2026-07-09_focusoffset_warning

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📊 Report Overview

Event Metadata

Record Type
Qc Session

Reason / Suite
Monthly_qc

Operator
Elina Vainio

Instrument
scope-testx1

QC Summary & Evaluation

Summary: QC trended increased objective-dependent focus offset before turret cleaning.

WARN

psf.60x_oil.525.fwhm_z_nm: Focus offset proxy in warning band; cleaning and recalibration initiated.

🔬 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.

🔦 Laser Measurement Context

Field	Value
Measurement position	at objective
Position details	60x/1.4 objective with calibrated photodiode adapter.
Power meter	Thorlabs PM100D + S170C
Power meter serial	PMD-AX41-228
Calibration due	2026-12-31
Integration time	1 s
Power meter notes	Room temp 22 C, humidity 41%.

📏 QC Measurements

Measurement	Value	Source	Details
488 nm laser power at objective (10%) `laser.at_obj.488.10pct.power_mw`	0.22 mW	Laser linearity input	Single sweep after 10-minute warm-up.
488 nm laser power at objective (20%) `laser.at_obj.488.20pct.power_mw`	0.44 mW	Laser linearity input	Single sweep after 10-minute warm-up.
488 nm laser power at objective (50%) `laser.at_obj.488.50pct.power_mw`	1.1 mW	Laser linearity input	Single sweep after 10-minute warm-up.
488 nm laser power at objective (100%) `laser.at_obj.488.100pct.power_mw`	2.18 mW	Laser linearity input	Single sweep after 10-minute warm-up.
488 nm laser power at objective (80%) at t=0 s `laser.at_obj.488.80pct.stability_t0s.power_mw`	1.75 mW	Laser stability input	Short-term stability check for trend continuity. Sampling: 1 Hz for 5 min
488 nm laser power at objective (80%) at t=120 s `laser.at_obj.488.80pct.stability_t120s.power_mw`	1.74 mW	Laser stability input	Short-term stability check for trend continuity. Sampling: 1 Hz for 5 min
488 nm laser power at objective (80%) at t=300 s `laser.at_obj.488.80pct.stability_t300s.power_mw`	1.75 mW	Laser stability input	Short-term stability check for trend continuity. Sampling: 1 Hz for 5 min
Visual · Optics Clean `visual.optics_clean`	yes	Human input	No visible residue on objective front lens.
Laser · 488 · Linearity R² `laser.488.linearity_r2`	0.997	Computed metric	—
PSF · 60x Oil · 525 · FWHM XY Max nm `psf.60x_oil.525.fwhm_xy_max_nm`	240 nm	Computed metric	—
PSF · 60x Oil · 525 · FWHM XY Min nm `psf.60x_oil.525.fwhm_xy_min_nm`	240 nm	Computed metric	—
PSF · 60x Oil · 525 · FWHM Z nm `psf.60x_oil.525.fwhm_z_nm`	630 nm	Computed metric	—
Chromatic Shift · 60x Oil · 561 To 488 · Dist nm `chromatic_shift.60x_oil.561_to_488.dist_nm`	80 nm	Computed metric	—
Stage · Repeatability Sigma X nm `stage.repeatability_sigma_x_nm`	220 nm	Computed metric	—
Stage · Repeatability Sigma Y nm `stage.repeatability_sigma_y_nm`	230 nm	Computed metric	—

📎 Artifacts & References

Artifact ID	Role	Description
`art_laser_linearity_csv`	TABLE	Laser setpoint sweep.: `omero://aic-core/scope-testx1/2026/dataset/qc_scope-testx1_20260709T0930Z_focusoffset_v1/laser_linearity.csv`
`art_laser_stability_csv`	TABLE	Laser stability time series.: `omero://aic-core/scope-testx1/2026/dataset/qc_scope-testx1_20260709T0930Z_focusoffset_v1/laser_stability.csv`
`art_psf_stack_raw`	RAW_IMAGE	PSF bead stack.: `omero://aic-core/scope-testx1/2026/image/qc_scope-testx1_20260709T0930Z_focusoffset_v1_psf`
`art_psf_preview`	PREVIEW	PSF MIP preview.: `qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20260709T0930Z_focusoffset_v1_psf_mip.png`
`art_coreg_stack_raw`	RAW_IMAGE	Co-registration stack.: `omero://aic-core/scope-testx1/2026/image/qc_scope-testx1_20260709T0930Z_focusoffset_v1_coreg`
`art_coreg_preview`	PREVIEW	Co-registration overlay preview.: `qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20260709T0930Z_focusoffset_v1_coreg_overlay.png`
`art_stage_repeat_raw`	RAW_IMAGE	Stage repeatability acquisition.: `omero://aic-core/scope-testx1/2026/image/qc_scope-testx1_20260709T0930Z_focusoffset_v1_stage`
`art_stage_repeat_plot`	PREVIEW	Stage repeatability plot.: `qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20260709T0930Z_focusoffset_v1_stage_repeat.png`

Additional Notes

Offset largest on 60x objective after frequent switching; turret contacts showed visible residue.

📄 Raw YAML Ledger

View 2026-07-09_focusoffset_warning.yaml

schema_version: 1
record_type: qc_session
qc_id: qc_scope-testx1_20260709T0930Z_focusoffset_v1
microscope: scope-testx1
started_utc: '2026-07-09T09:30:00Z'
ended_utc: '2026-07-09T10:10:00Z'
reason: monthly_qc
summary: QC trended increased objective-dependent focus offset before turret cleaning.
notes: 'Offset largest on 60x objective after frequent switching; turret contacts
  showed visible residue.

  '
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: 2.18
    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: '2026-07-09T10:10:00Z'
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: 630
  unit: nm
  metric_class: fwhm_axial
- metric_id: chromatic_shift.60x_oil.561_to_488.dist_nm
  value: 80
  unit: nm
  metric_class: chromatic_shift
- metric_id: stage.repeatability_sigma_x_nm
  value: 220
  unit: nm
  metric_class: stage_repeatability
- metric_id: stage.repeatability_sigma_y_nm
  value: 230
  unit: nm
  metric_class: stage_repeatability
evaluation:
  benchmark_ref: benchmarks/scope-testx1.yaml@main
  evaluated_utc: '2026-07-09T10:10:00Z'
  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: Focus offset proxy in warning band; cleaning and recalibration initiated.
artifacts:
- artifact_id: art_laser_linearity_csv
  role: table
  uri: omero://aic-core/scope-testx1/2026/dataset/qc_scope-testx1_20260709T0930Z_focusoffset_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_20260709T0930Z_focusoffset_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_20260709T0930Z_focusoffset_v1_psf
  description: PSF bead stack.
- artifact_id: art_psf_preview
  role: preview
  uri: qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20260709T0930Z_focusoffset_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_20260709T0930Z_focusoffset_v1_coreg
  description: Co-registration stack.
- artifact_id: art_coreg_preview
  role: preview
  uri: qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20260709T0930Z_focusoffset_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_20260709T0930Z_focusoffset_v1_stage
  description: Stage repeatability acquisition.
- artifact_id: art_stage_repeat_plot
  role: preview
  uri: qc/sessions/scope-testx1/2026/previews/qc_scope-testx1_20260709T0930Z_focusoffset_v1_stage_repeat.png
  description: Stage repeatability plot.
performed_by: Elina Vainio