[Feature] Asynchronous dynamic timelapse with per-embryo independent scheduling

[pskeshu]

Description

Enhance the existing TimelapseOrchestrator to support truly asynchronous, dynamically configurable timelapse acquisition where each embryo operates on independent schedules that can be modified at runtime.

Current State

• TimelapseOrchestrator exists with background asyncio task
• Per-embryo EmbryoAcquisitionState tracks intervals and timepoints
• Stop conditions and interval rules exist but are set at start time

Requirements

1. Independent Embryo Scheduling

Each embryo should have its own acquisition schedule that can be started/stopped/modified independently without affecting others.

2. Dynamic Configuration

Allow runtime modification of:

• Acquisition intervals per embryo
• Number of slices, exposure settings
• Stop conditions (add/remove/modify)
• Priority ordering
• Focus drift correction parameters

3. Spawn-on-Demand

Ability to add new embryos to an ongoing timelapse without restarting.

4. Asynchronous Event Handling

• Detection-triggered interval changes should apply immediately
• Stage-based adaptive imaging (speed up before hatching)

5. Fluorescence Signal-Driven Acquisition

• Monitor embryos periodically (low frequency) for fluorescence signal expression (e.g., red channel)
• When signal starts expressing, automatically increase imaging frequency for that embryo
• Support configurable signal thresholds and frequency escalation rules
• Use case: Late-expressing reporters where expression timing varies per embryo

Technical Approach

• Refactor TimelapseOrchestrator._run_loop() to use per-embryo asyncio tasks instead of sequential loop
• Add EmbryoTimelapseTask class managing individual embryo acquisition lifecycle
• Add real-time configuration update API via tools
• Implement FluorescenceMonitor for signal-triggered acquisition:
  • Periodic low-frequency monitoring task (configurable interval)
  • Signal detection via intensity thresholding or detector system
  • Automatic interval adjustment rules when signal detected
  • Per-embryo signal tracking state

Key Files

• gently/agent/timelapse_orchestrator.py
• gently/agent/state.py (EmbryoAcquisitionState)
• gently/agent/tools/timelapse_tools.py