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Suggested Protocols

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Imaging & Analysis — Fixed-cell Fluorescence Foundation

Imaging with lineage preserved from acquisition to interpretation handoff

Trace the specimen handoff, acquisition, immutable raw artifact, processing, segmentation, measurement, replicate summary, and interpretation handoff.

Editable starter protocols

4 source-bound starters

What do these protocols do?

They lock specimen and acquisition settings, link raw and processed artifacts through parent lineage, and create explicit background, measurement, replicate, and colocalization receipts.

Supported imaging workflows

  • • Common specimen, artifact & replicate contract
  • • Fixed-cell fluorescence acquisition record
  • • Artifact, processing & quantification lineage
  • • Fluorescence spatial-association analysis

Scope boundary

They do not upload images, hide downsampling, run AI segmentation, coerce widefield with confocal or fields with biological replicates, or declare a universal image/biological PASS or molecular interaction.

PRT-IMG-COMMON-001Common specimen, artifact & replicate contract

Fixed-cell fluorescence specimen, acquisition, artifact and replicate lineage contract

Imaging & Analysis · IMG-FAMILY-CONTRACT-1.0

Official guidance reviewed
FIXED_CELL_FLUORESCENCE_FIRST_CHILDIMMUTABLE_RAW_ARTIFACTEXPLICIT_PARENT_AND_PROCESSING_REVISIONWIDEFIELD_AND_CONFOCAL_NOT_COERCEDREPLICATE_LEVELS_NOT_POOLEDEXCLUSIONS_ARE_APPEND_ONLY_LEDGER_ROWSNO_UNIVERSAL_IMAGE_OR_BIOLOGICAL_PASSCOLOCALIZATION_IS_NOT_INTERACTIONNO_SERVER_UPLOAD_OR_HIDDEN_DOWNSAMPLE_OR_AI

Lock lineage before interpreting an image

Keep widefield and confocal settings distinct, connect every derived artifact to its raw parent, and never treat fields as biological replicates or colocalization as interaction.

1

1. VALIDATE SPECIMEN HANDOFF

Import only minimum specimen identity, staining receipt, preparation revision, groups, controls and unknowns; never copy the staining recipe.

2

2. DECLARE QUESTION AND REPLICATE LEVELS

Predeclare experiment, biological replicate, technical replicate, field and object identities without treating fields as independent biological replicates.

3

3. LOCK MODALITY AND INSTRUMENT

Select widefield, laser-scanning confocal or spinning-disk confocal and record exact instrument, objective, detector and channel identities.

4

4. CAPTURE ACQUISITION SETTINGS

Record pixel calibration, z geometry, bit depth, exposure or dwell, gain, laser power, order, sampling plan and saturation disposition.

5

5. FREEZE RAW ARTIFACT

Create an immutable raw artifact identity with checksum and dimensions. A raw artifact cannot name a processed parent.

6

6. APPEND PROCESSING AND EXCLUSIONS

Every derived artifact names one parent, operation, parameters and software revision; exclusions remain rows with reason and actor.

7

7. SUMMARIZE WITHOUT PSEUDOREPLICATION

Aggregate objects and fields within their explicit hierarchy, then technical replicates within biological replicates; never silently pool levels.

8

8. ISSUE INTERPRETATION HANDOFF

Export measurements, setting mismatches, controls, caveats and unknowns. Do not emit a universal image-quality or biological PASS.