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QC session · 2025-10-09

Nikon Ti2-E Crest V3

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Event overview

Event metadata
Record type
QC session
Reason / suite
Routine PSF check
Operator
AIC Staff
Record ID
2025-10-09_psf_check
QC summary and evaluation

Summary: Automated PSF extraction for 60x Silicone, 60x Oil, and 100x Oil objectives using Turku CIC Nikon Crest v3.

PASS
psf.60x_oil.525.fwhm_z_nm: 60x oil axial PSF remained within expected range.

Tests performed

Test type Details
Psf Sub-diffraction beads measured on 60x Silicone, 60x Oil, and 100x Oil.

Laser measurement context

Field Value
Measurement position at objective
Position details Not measured in this PSF-only session.
Power meter not_applicable
Power meter notes Laser power linearity/stability was not part of this session.

QC measurements

Measurement Value Source Details
Environment · Room Temperature C
environment.room_temperature_c		 20 celsius Human input Recorded from PSF report metadata.
PSF · 60x Silicone · 525 · FWHM XY Max nm
psf.60x_silicone.525.fwhm_xy_max_nm		 288.3 nm Computed metric StdDev: 4.9. N=93 beads.
PSF · 60x Silicone · 525 · FWHM XY Min nm
psf.60x_silicone.525.fwhm_xy_min_nm		 267.1 nm Computed metric —
PSF · 60x Silicone · 525 · FWHM Z nm
psf.60x_silicone.525.fwhm_z_nm		 853.2 nm Computed metric —
PSF · 60x Silicone · 525 · Asymmetry
psf.60x_silicone.525.asymmetry		 0.93 Computed metric —
Chromatic Shift · 60x Silicone · 425 To 525 · Z nm
chromatic_shift.60x_silicone.425_to_525.z_nm		 127.5 nm Computed metric Axial shift of Blue 425 relative to Green 525.
PSF · 60x Oil · 525 · FWHM XY Max nm
psf.60x_oil.525.fwhm_xy_max_nm		 291.1 nm Computed metric StdDev: 7.6. N=356 beads.
PSF · 60x Oil · 525 · FWHM XY Min nm
psf.60x_oil.525.fwhm_xy_min_nm		 260.2 nm Computed metric —
PSF · 60x Oil · 525 · FWHM Z nm
psf.60x_oil.525.fwhm_z_nm		 686.8 nm Computed metric —
PSF · 60x Oil · 525 · Asymmetry
psf.60x_oil.525.asymmetry		 0.93 Computed metric —
Chromatic Shift · 60x Oil · 425 To 525 · Z nm
chromatic_shift.60x_oil.425_to_525.z_nm		 118.7 nm Computed metric Axial shift of Blue 425 relative to Green 525.
PSF · 100x Oil · 525 · FWHM XY Max nm
psf.100x_oil.525.fwhm_xy_max_nm		 210 nm Computed metric StdDev: 1.5. N=85 beads.
PSF · 100x Oil · 525 · FWHM XY Min nm
psf.100x_oil.525.fwhm_xy_min_nm		 203.1 nm Computed metric —
PSF · 100x Oil · 525 · FWHM Z nm
psf.100x_oil.525.fwhm_z_nm		 585.5 nm Computed metric —
PSF · 100x Oil · 525 · Asymmetry
psf.100x_oil.525.asymmetry		 0.97 Computed metric —
Chromatic Shift · 100x Oil · 425 To 525 · Z nm
chromatic_shift.100x_oil.425_to_525.z_nm		 -25.4 nm Computed metric Axial shift of Blue 425 relative to Green 525.

Artifacts and references

Artifact ID Role Description
art_psf_60x_silicone RAW_IMAGE Raw z-stack for PLAN APO 60x SIL.: omero:////image/
art_psf_60x_oil RAW_IMAGE Raw z-stack for PLAN APO AD 60x OIL.: omero:////image/
art_psf_100x_oil RAW_IMAGE Raw z-stack for PLAN APO AD 100x OIL.: omero:////image/

Additional notes

Images acquired at room temperature (20°C). Measurements extracted using the ImageJ PSFj plugin.

Raw YAML record

View 2025-10-09_psf_check.yaml 
schema_version: 1
record_type: qc_session
qc_id: qc_scope-nikon-crest-v3_20251009T1000Z_psf_v1
microscope: scope-nikon-crest-v3
started_utc: '2025-10-09T10:00:00Z'
reason: routine_psf_check
summary: Automated PSF extraction for 60x Silicone, 60x Oil, and 100x Oil objectives
  using Turku CIC Nikon Crest v3.
notes: "Images acquired at room temperature (20\xB0C). Measurements extracted using\
  \ the ImageJ PSFj plugin."
performed:
- qc_type: psf
  details: Sub-diffraction beads measured on 60x Silicone, 60x Oil, and 100x Oil.
  artifacts:
  - art_psf_60x_silicone
  - art_psf_60x_oil
  - art_psf_100x_oil
inputs_human:
- metric_id: environment.room_temperature_c
  value: 20
  unit: celsius
  details: Recorded from PSF report metadata.
  metric_class: signal_to_noise
laser_inputs_human:
  measurement_position: at_objective
  measurement_position_details: Not measured in this PSF-only session.
  power_meter:
    model: not_applicable
    serial: ''
    calibration_due: ''
    notes: Laser power linearity/stability was not part of this session.
  linearity_series: []
  stability_series: []
computed_provenance:
  pipeline: imagej_psfj
  version: unknown
  run_utc: '2025-10-09T14:02:00Z'
metrics_computed:
- metric_id: psf.60x_silicone.525.fwhm_xy_max_nm
  value: 288.3
  unit: nm
  details: 'StdDev: 4.9. N=93 beads.'
  metric_class: fwhm_lateral
- metric_id: psf.60x_silicone.525.fwhm_xy_min_nm
  value: 267.1
  unit: nm
  metric_class: fwhm_lateral
- metric_id: psf.60x_silicone.525.fwhm_z_nm
  value: 853.2
  unit: nm
  metric_class: fwhm_axial
- metric_id: psf.60x_silicone.525.asymmetry
  value: 0.93
  unit: unitless
  metric_class: fwhm_lateral
- metric_id: chromatic_shift.60x_silicone.425_to_525.z_nm
  value: 127.5
  unit: nm
  details: Axial shift of Blue 425 relative to Green 525.
  metric_class: chromatic_shift
- metric_id: psf.60x_oil.525.fwhm_xy_max_nm
  value: 291.1
  unit: nm
  details: 'StdDev: 7.6. N=356 beads.'
  metric_class: fwhm_lateral
- metric_id: psf.60x_oil.525.fwhm_xy_min_nm
  value: 260.2
  unit: nm
  metric_class: fwhm_lateral
- metric_id: psf.60x_oil.525.fwhm_z_nm
  value: 686.8
  unit: nm
  metric_class: fwhm_axial
- metric_id: psf.60x_oil.525.asymmetry
  value: 0.93
  unit: unitless
  metric_class: fwhm_lateral
- metric_id: chromatic_shift.60x_oil.425_to_525.z_nm
  value: 118.7
  unit: nm
  details: Axial shift of Blue 425 relative to Green 525.
  metric_class: chromatic_shift
- metric_id: psf.100x_oil.525.fwhm_xy_max_nm
  value: 210.0
  unit: nm
  details: 'StdDev: 1.5. N=85 beads.'
  metric_class: fwhm_lateral
- metric_id: psf.100x_oil.525.fwhm_xy_min_nm
  value: 203.1
  unit: nm
  metric_class: fwhm_lateral
- metric_id: psf.100x_oil.525.fwhm_z_nm
  value: 585.5
  unit: nm
  metric_class: fwhm_axial
- metric_id: psf.100x_oil.525.asymmetry
  value: 0.97
  unit: unitless
  metric_class: fwhm_lateral
- metric_id: chromatic_shift.100x_oil.425_to_525.z_nm
  value: -25.4
  unit: nm
  details: Axial shift of Blue 425 relative to Green 525.
  metric_class: chromatic_shift
evaluation:
  benchmark_ref: benchmarks/scope-nikon-crest-v3.yaml@main
  evaluated_utc: '2025-10-09T14:10:00Z'
  evaluated_by: github_action:qceval
  overall_status: pass
  results:
  - metric_id: psf.60x_oil.525.fwhm_z_nm
    status: pass
    threshold: warn>750nm, fail>900nm
    message: 60x oil axial PSF remained within expected range.
artifacts:
- artifact_id: art_psf_60x_silicone
  role: raw_image
  uri: omero://<server>/<group>/image/<id>
  description: Raw z-stack for PLAN APO 60x SIL.
- artifact_id: art_psf_60x_oil
  role: raw_image
  uri: omero://<server>/<group>/image/<id>
  description: Raw z-stack for PLAN APO AD 60x OIL.
- artifact_id: art_psf_100x_oil
  role: raw_image
  uri: omero://<server>/<group>/image/<id>
  description: Raw z-stack for PLAN APO AD 100x OIL.
performed_by: AIC Staff