📝 Event: 2025-10-09_psf_check

📊 Report Overview

Event Metadata

Record Type
Qc Session

Reason / Suite
Routine_psf_check

Operator
AIC Staff

Instrument
scope-nikon-crest-v3

QC Summary & Evaluation

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

PASS

🔬 Tests Performed

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

📏 Computed Metrics

Metric ID	Value
`psf.60x_silicone.525.fwhm_xy_max_nm`	288.3
`psf.60x_silicone.525.fwhm_xy_min_nm`	267.1
`psf.60x_silicone.525.fwhm_z_nm`	853.2
`psf.60x_silicone.525.asymmetry`	0.93
`chromatic_shift.60x_silicone.425_to_525.z_nm`	127.5
`psf.60x_oil.525.fwhm_xy_max_nm`	291.1
`psf.60x_oil.525.fwhm_xy_min_nm`	260.2
`psf.60x_oil.525.fwhm_z_nm`	686.8
`psf.60x_oil.525.asymmetry`	0.93
`chromatic_shift.60x_oil.425_to_525.z_nm`	118.7
`psf.100x_oil.525.fwhm_xy_max_nm`	210.0
`psf.100x_oil.525.fwhm_xy_min_nm`	203.1
`psf.100x_oil.525.fwhm_z_nm`	585.5
`psf.100x_oil.525.asymmetry`	0.97
`chromatic_shift.100x_oil.425_to_525.z_nm`	-25.4

📎 Artifacts & 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 Ledger

View 2025-10-09_psf_check.yaml

schema_version: 1
record_type: qc_session

# -----------------------------------------------------------------------------
# Identity and timing
# -----------------------------------------------------------------------------
qc_id: "qc_scope-nikon-crest-v3_20251009T100000Z_psf"
microscope: "scope-nikon-crest-v3"                   # Matches the instrument_id exactly

started_utc: "2025-10-09T10:00:00Z"                  # Extracted from PDF Date of Acquisition
performed_by: "AIC Staff"
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°C). Measurements extracted using the ImageJ PSFj plugin."

# -----------------------------------------------------------------------------
# What was performed 
# -----------------------------------------------------------------------------
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"]

# -----------------------------------------------------------------------------
# HUMAN INPUTS 
# -----------------------------------------------------------------------------
inputs_human:
  - metric_id: "environment.room_temperature_c"
    value: 20
    unit: "C"
    details: "Recorded from PSF report metadata."

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 METRICS (Generated via ImageJ)
# -----------------------------------------------------------------------------
computed_provenance:
  pipeline: "imagej_psfj"                            # Corrected to reflect ImageJ PSFj
  version: "unknown"                                 # Update if you know the exact plugin version
  run_utc: "2025-10-09T14:02:00Z"                    

metrics_computed:

  # ==========================================
  # OBJECTIVE: 60x Silicone (ID: 60x_silicone)
  # ==========================================
  - metric_id: "psf.60x_silicone.525.fwhm_xy_max_nm"
    value: 288.3
    unit: "nm"
    details: "StdDev: 4.9. N=93 beads."

  - metric_id: "psf.60x_silicone.525.fwhm_xy_min_nm"
    value: 267.1
    unit: "nm"

  - metric_id: "psf.60x_silicone.525.fwhm_z_nm"
    value: 853.2
    unit: "nm"

  - metric_id: "psf.60x_silicone.525.asymmetry"
    value: 0.93
    unit: "unitless"

  - 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."

  # ==========================================
  # OBJECTIVE: 60x Oil (ID: 60x_oil)
  # ==========================================
  - metric_id: "psf.60x_oil.525.fwhm_xy_max_nm"
    value: 291.1
    unit: "nm"
    details: "StdDev: 7.6. N=356 beads."

  - metric_id: "psf.60x_oil.525.fwhm_xy_min_nm"
    value: 260.2
    unit: "nm"

  - metric_id: "psf.60x_oil.525.fwhm_z_nm"
    value: 686.8
    unit: "nm"

  - metric_id: "psf.60x_oil.525.asymmetry"
    value: 0.93
    unit: "unitless"

  - 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."

  # ==========================================
  # OBJECTIVE: 100x Oil (ID: 100x_oil)
  # ==========================================
  - metric_id: "psf.100x_oil.525.fwhm_xy_max_nm"
    value: 210.0
    unit: "nm"
    details: "StdDev: 1.5. N=85 beads."

  - metric_id: "psf.100x_oil.525.fwhm_xy_min_nm"
    value: 203.1
    unit: "nm"

  - metric_id: "psf.100x_oil.525.fwhm_z_nm"
    value: 585.5
    unit: "nm"

  - metric_id: "psf.100x_oil.525.asymmetry"
    value: 0.97
    unit: "unitless"

  - 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."

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: []

# -----------------------------------------------------------------------------
# ARTIFACT POINTERS 
# -----------------------------------------------------------------------------
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."