[Documentation] Document conceptual framework for sample tracking, hardware abstraction, and generalizable metrics

[pskeshu]

Description

Document the conceptual framework for how different microscope modalities map to standardized operations, and establish generalizable sample tracking metrics that apply across sample types.

Current State

• Hardcoded for DiSPIM hardware (specific device names)
• Sample model is embryo-specific
• Bottom camera = sample overview (DiSPIM-specific concept)
• Sample tracking metrics (exposure, focus) exist but are embryo-specific

Scope (DiSPIM Focus)

This issue focuses on documenting the conceptual mapping without implementing full abstraction:

1. Document Conceptual Equivalences

DiSPIM Operation	General Concept	Other Modality Examples
Bottom camera view	Sample overview	10x widefield, low-mag confocal
Lightsheet volume	3D acquisition	Confocal z-stack, widefield decon
Embryo detection	Sample detection	Well detection, cell segmentation
Stage calibration	Position calibration	Same across modalities

2. Standardized Bluesky Plan Naming

• Keep DiSPIM implementations, but use generalizable names
• sample_overview_plan() → current bottom camera plan
• focus_scan_plan() → current FFT focus sweep
• acquire_volume_plan() → current lightsheet volume
• Future modalities implement same-named plans

3. Generalizable Sample Tracking Metrics

Document which per-sample metrics are universal vs domain-specific:

Metric	Description	Generalizability
total_light_exposure_ms	Cumulative illumination time	Universal
exposure_count	Number of acquisitions	Universal
photobleaching_curve	Intensity decay over time	Universal (fluorescence)
focus_drift_rate	µm/hour drift estimate	Universal
focus_history	Historical focus positions	Universal
position_history	Stage position over time	Universal
signal_intensity_history	Per-channel intensity	Universal (fluorescence)
developmental_stage	Sample maturity state	Domain-specific
morphology_metrics	Shape/size measurements	Domain-specific

4. Configuration Documentation

• Document which DiSPIM devices map to which conceptual roles
• Create template for future hardware profiles
• Sample tracking metric schema

Deliverables

• Architecture decision record (ADR) documenting the conceptual framework
• README section on "Extending to Other Microscopes"
• Plan naming convention guide
• Hardware capability mapping template
• Sample tracking metrics specification

Key Files

• New: docs/architecture/sample-hardware-domains.md
• New: docs/architecture/sample-tracking-metrics.md
• Update: README.md (extension section)
• Update: gently/plans.py (add docstrings with conceptual mappings)