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Light panel: illumination mode is the root of the control #164

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d63af5d
Light panel: illumination mode is the root of the control
pskeshu Sep 6, 2026
f8eeaa1
Calibration closes the LED before it looks at anything (#106)
pskeshu Sep 6, 2026
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99 changes: 99 additions & 0 deletions .claude/skills/gently-debugging/SKILL.md
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---
name: gently-debugging
description: Use when debugging a Gently session, inspecting stored data, or tailing logs — the full D:/Gently3 file-store directory layout, log locations/tail commands, and the map of debugging data sources (traces, predictions, memory, session/timelapse state).
---

# Gently — debugging & data-source reference

The Gently3 store is file-based under `D:\Gently3\` (env: `GENTLY_STORAGE_PATH`). No SQLite — everything is human-browsable files. See the resident `CLAUDE.md` for the store classes and architecture summary; this skill holds the full layout and debugging map.

## Directory layout

```
D:/Gently3/
gently.yaml # root manifest
sessions/
_index.yaml # session_id -> folder_name mapping
{YYYYMMDD}_{HHMM}_{slug}_{id8}/
session.yaml # metadata, config, organism
session.lock # PID + hostname (while active)
intent.yaml # planned vs actual
timelapse.yaml # checkpointed timelapse state
timeline.jsonl # session events
interaction_log.jsonl # agent conversation records
conversation.json # Claude API messages (resumption)
summary.yaml # auto-generated stats
perception_runs.yaml # run metadata
snapshots/{source}_{stem}.tif
embryos/{embryo_id}/
embryo.yaml # position, calibration, uid
predictions.jsonl # per-timepoint summary
ground_truth.yaml # human annotations
timelapse.mp4
volumes/t{NNNN}.tif
volumes/t{NNNN}.meta.yaml # shape, dtype, acquired_at, metadata
projections/t{NNNN}.jpg
traces/t{NNNN}.json # complete perception record
agent/
state.yaml # key-value agent state
campaigns/{id}_{slug}/
campaign.yaml
plan/current.yaml
plan/history/{YYYYMMDD_HHMM}.yaml
templates/{name}.yaml
projects/{id}_{slug}.yaml
session_intents/{session_id}.yaml
planned_sessions/{id}.yaml
learnings/{id}_{slug}.yaml
observations/{id}_{slug}.yaml
active/expectations.yaml
active/watchpoints.yaml
active/questions.yaml
embryo_understanding/{uid}.yaml
ml/pipelines/{id}.yaml
ml/runs/{id}.yaml
ml/assessments/{id}.yaml
logs/
gently_{YYYYMMDD_HHMMSS}.log
device_layer_{YYYYMMDD_HHMMSS}.log
config/
hardware.yaml
mesh/...
incoming/{uuid}.tif # transient device staging
```

### Legacy stores (D:\Gently2\ — read-only reference)
The old SQLite-based stores are preserved but no longer written to:
- `gently.db` (GentlyStore) — replaced by FileStore
- `context/agent_mind.db` (ContextStore) — replaced by FileContextStore
- `D:\gently\dataset.db` — legacy benchmarking DB

## Logging

Both the agent and device layer write logs to `D:\Gently3\logs\`:

- **Agent**: `gently_YYYYMMDD_HHMMSS.log` — INFO+ to file, console level configurable via `-v` flag
- **Device layer**: `device_layer_YYYYMMDD_HHMMSS.log` — INFO level

To check logs during a session:
```bash
# Latest agent log
tail -f D:/Gently3/logs/$(ls -t D:/Gently3/logs/gently_*.log | head -1)

# Latest device layer log
tail -f D:/Gently3/logs/$(ls -t D:/Gently3/logs/device_layer_*.log | head -1)

# Filter for errors
grep -E "ERROR|Traceback" D:/Gently3/logs/gently_*.log
```

## Debugging Data Sources

- **Agent logs**: `D:\Gently3\logs\gently_*.log`
- **Device layer logs**: `D:\Gently3\logs\device_layer_*.log`
- **Perception traces**: `D:\Gently3\sessions\{session}\embryos\{embryo}\traces\` — per-timepoint JSON
- **Predictions**: `D:\Gently3\sessions\{session}\embryos\{embryo}\predictions.jsonl`
- **Volume staging**: `D:\Gently3\incoming\`
- **Agent memory**: `D:\Gently3\agent\` — campaigns, learnings, observations (all YAML)
- **Session state**: `D:\Gently3\sessions\{session}\session.yaml`
- **Timelapse state**: `D:\Gently3\sessions\{session}\timelapse.yaml`
55 changes: 55 additions & 0 deletions .playwright-mcp/page-2026-08-24T08-24-47-321Z.yml
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- generic [active] [ref=e1]:
- generic [ref=e2]:
- generic:
- generic [ref=e3]: BOTTOM CAMERA
- generic [ref=e9]:
- generic [ref=e10]: EMBRYOS · 4
- generic [ref=e13]:
- generic [ref=e14]:
- generic [ref=e15] [cursor=pointer]: e01 1420, 880
- generic [ref=e16] [cursor=pointer]: e02 1610, 905
- generic [ref=e17] [cursor=pointer]: e03 1755, 1120
- generic [ref=e18] [cursor=pointer]: e04 2010, 860
- generic [ref=e19]:
- button "remap region" [ref=e20] [cursor=pointer]
- generic [ref=e21]: µm
- generic [ref=e22]:
- generic [ref=e23]: SPIM HEAD
- generic [ref=e26]:
- generic [ref=e27]:
- generic [ref=e28]: laser
- slider [ref=e29]: "35"
- generic [ref=e30]: 35%
- generic [ref=e31]:
- generic [ref=e32]: exposure
- slider [ref=e33]: "40"
- generic [ref=e34]: 40ms
- generic [ref=e35]:
- generic [ref=e36]: step
- slider [ref=e37]: "50"
- generic [ref=e38]: 50µm
- generic [ref=e39]:
- button "go to e02" [ref=e40] [cursor=pointer]
- button "HALT" [ref=e41] [cursor=pointer]
- generic [ref=e42]:
- generic [ref=e43]: STAGE
- generic [ref=e46]:
- generic [ref=e47]:
- generic [ref=e48]: x
- generic [ref=e49]: 1610.4 µm
- generic [ref=e50]:
- generic [ref=e51]: "y"
- generic [ref=e52]: 905.2 µm
- generic [ref=e53]:
- generic [ref=e54]: z
- generic [ref=e55]: "-12.8 µm"
- generic [ref=e56]:
- button "snap" [ref=e57] [cursor=pointer]
- button "live" [ref=e58] [cursor=pointer]
- generic [ref=e59]: drag empty space to pan · wheel to zoom · f fit · 1 100%
- generic [ref=e60]:
- button "+ calibration" [ref=e61] [cursor=pointer]
- button "+ agent" [ref=e62] [cursor=pointer]
- button "+ acquisition" [ref=e63] [cursor=pointer]
- button "fit" [ref=e64] [cursor=pointer]
- generic [ref=e65]: 132%
119 changes: 119 additions & 0 deletions .playwright-mcp/page-2026-08-24T08-31-44-879Z.yml
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- generic [active] [ref=f1e1]:
- generic [ref=f1e2]:
- generic:
- generic [ref=f1e3]:
- generic [ref=f1e4]:
- generic [ref=f1e5]: EMBRYOS · 4
- generic [ref=f1e6]: live
- generic [ref=f1e7]:
- generic [ref=f1e8]:
- generic [ref=f1e9] [cursor=pointer]: e01 1420, 880
- generic [ref=f1e10] [cursor=pointer]: e02 1610, 905
- generic [ref=f1e11] [cursor=pointer]: e03 1755, 1120
- generic [ref=f1e12] [cursor=pointer]: e04 2010, 860
- generic [ref=f1e13]:
- button "remap region" [ref=f1e14] [cursor=pointer]
- generic [ref=f1e15]: µm
- generic [ref=f1e16]:
- generic [ref=f1e17]:
- generic [ref=f1e18]: BOTTOM CAMERA
- generic [ref=f1e19]: live
- generic [ref=f1e23]:
- button "−" [ref=f1e24] [cursor=pointer]
- generic [ref=f1e25]: 1.0×
- button "+" [ref=f1e26] [cursor=pointer]
- generic [ref=f1e27]:
- generic [ref=f1e28]:
- generic [ref=f1e29]: SPIM HEAD
- generic [ref=f1e30]: ready
- generic [ref=f1e31]:
- generic [ref=f1e32]:
- generic [ref=f1e33]: laser
- slider [ref=f1e34]: "35"
- generic [ref=f1e35]: 35%
- generic [ref=f1e36]:
- generic [ref=f1e37]: exposure
- slider [ref=f1e38]: "40"
- generic [ref=f1e39]: 40ms
- generic [ref=f1e40]:
- generic [ref=f1e41]: step
- slider [ref=f1e42]: "50"
- generic [ref=f1e43]: 50µm
- generic [ref=f1e44]:
- button "go to e02" [ref=f1e45] [cursor=pointer]
- button "HALT" [ref=f1e46] [cursor=pointer]
- generic [ref=f1e47]:
- generic [ref=f1e48]:
- generic [ref=f1e49]: STAGE
- generic [ref=f1e50]: live
- generic [ref=f1e51]:
- generic [ref=f1e52]:
- generic [ref=f1e53]: x
- generic [ref=f1e54]: 1610.4 µm
- generic [ref=f1e55]:
- generic [ref=f1e56]: "y"
- generic [ref=f1e57]: 905.2 µm
- generic [ref=f1e58]:
- generic [ref=f1e59]: z
- generic [ref=f1e60]: "-12.8 µm"
- generic [ref=f1e61]:
- generic [ref=f1e62]:
- generic [ref=f1e63]: CALIBRATION · two-point
- generic [ref=f1e64]: stale
- generic [ref=f1e65]:
- generic [ref=f1e66]:
- generic [ref=f1e67]: source
- generic [ref=f1e68]: laser 488
- generic [ref=f1e69]:
- generic [ref=f1e70]: point 1
- generic [ref=f1e71]: captured
- generic [ref=f1e72]:
- generic [ref=f1e73]: point 2
- generic [ref=f1e74]: —
- generic [ref=f1e75]:
- button "capture point 2" [ref=f1e76] [cursor=pointer]
- button "solve transform" [ref=f1e77] [cursor=pointer]
- generic [ref=f1e78]:
- generic [ref=f1e79]:
- generic [ref=f1e80]: ACQUISITION
- generic [ref=f1e81]: ready
- generic [ref=f1e82]:
- generic [ref=f1e83]:
- generic [ref=f1e84]: interval
- slider [ref=f1e85]: "100"
- generic [ref=f1e86]: 120s
- generic [ref=f1e87]:
- generic [ref=f1e88]: timepoints
- slider [ref=f1e89]: "60"
- generic [ref=f1e90]: "60"
- button "start" [ref=f1e92] [cursor=pointer]
- generic [ref=f1e93]:
- generic [ref=f1e94]:
- generic [ref=f1e95]: CURATOR
- generic [ref=f1e96]: live
- generic [ref=f1e97]:
- generic [ref=f1e98]:
- generic [ref=f1e99]: tracking
- generic [ref=f1e100]: e02 · bottom cam · stage
- generic [ref=f1e101]:
- generic [ref=f1e102]: stale
- generic [ref=f1e103]: calibration transform
- generic [ref=f1e104]: Calibration never completed. Acquisition would put e02 off-centre.
- generic [ref=f1e105]:
- button "show me" [ref=f1e106] [cursor=pointer]
- button "dismiss" [ref=f1e107] [cursor=pointer]
- generic [ref=f1e108]: "rule 5: keys 0–5 do this without me"
- generic [ref=f1e109]:
- generic [ref=f1e110]:
- generic [ref=f1e111]: EVENTS
- generic [ref=f1e112]: ready
- generic [ref=f1e113]: no events this session
- generic [ref=f1e115]: everything exists · attention travels · 0–5 · surface zoom ≠ frame zoom
- generic [ref=f1e116]:
- button "0 bench" [ref=f1e117] [cursor=pointer]
- button "1 detect" [ref=f1e118] [cursor=pointer]
- button "2 position" [ref=f1e119] [cursor=pointer]
- button "3 calibrate" [ref=f1e120] [cursor=pointer]
- button "4 acquire" [ref=f1e121] [cursor=pointer]
- button "5 curator" [ref=f1e122] [cursor=pointer]
- generic [ref=f1e123]: 182%
119 changes: 119 additions & 0 deletions .playwright-mcp/page-2026-08-24T08-32-07-503Z.yml
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- generic [ref=f1e1]:
- generic [ref=f1e2]:
- generic:
- generic [ref=f1e3]:
- generic [ref=f1e4]:
- generic [ref=f1e5]: EMBRYOS · 4
- generic [ref=f1e6]: live
- generic [ref=f1e7]:
- generic [ref=f1e8]:
- generic [ref=f1e9] [cursor=pointer]: e01 1420, 880
- generic [ref=f1e10] [cursor=pointer]: e02 1610, 905
- generic [ref=f1e11] [cursor=pointer]: e03 1755, 1120
- generic [ref=f1e12] [cursor=pointer]: e04 2010, 860
- generic [ref=f1e13]:
- button "remap region" [ref=f1e14] [cursor=pointer]
- generic [ref=f1e15]: µm
- generic [ref=f1e16]:
- generic [ref=f1e17]:
- generic [ref=f1e18]: BOTTOM CAMERA
- generic [ref=f1e19]: live
- generic [ref=f1e23]:
- button "−" [ref=f1e24] [cursor=pointer]
- generic [ref=f1e25]: 1.0×
- button "+" [ref=f1e26] [cursor=pointer]
- generic [ref=f1e27]:
- generic [ref=f1e28]:
- generic [ref=f1e29]: SPIM HEAD
- generic [ref=f1e30]: ready
- generic [ref=f1e31]:
- generic [ref=f1e32]:
- generic [ref=f1e33]: laser
- slider [ref=f1e34]: "35"
- generic [ref=f1e35]: 35%
- generic [ref=f1e36]:
- generic [ref=f1e37]: exposure
- slider [ref=f1e38]: "40"
- generic [ref=f1e39]: 40ms
- generic [ref=f1e40]:
- generic [ref=f1e41]: step
- slider [ref=f1e42]: "50"
- generic [ref=f1e43]: 50µm
- generic [ref=f1e44]:
- button "go to e02" [ref=f1e45] [cursor=pointer]
- button "HALT" [ref=f1e46] [cursor=pointer]
- generic [ref=f1e47]:
- generic [ref=f1e48]:
- generic [ref=f1e49]: STAGE
- generic [ref=f1e50]: live
- generic [ref=f1e51]:
- generic [ref=f1e52]:
- generic [ref=f1e53]: x
- generic [ref=f1e54]: 1610.4 µm
- generic [ref=f1e55]:
- generic [ref=f1e56]: "y"
- generic [ref=f1e57]: 905.2 µm
- generic [ref=f1e58]:
- generic [ref=f1e59]: z
- generic [ref=f1e60]: "-12.8 µm"
- generic [ref=f1e61]:
- generic [ref=f1e62]:
- generic [ref=f1e63]: CALIBRATION · two-point
- generic [ref=f1e64]: stale
- generic [ref=f1e65]:
- generic [ref=f1e66]:
- generic [ref=f1e67]: source
- generic [ref=f1e68]: laser 488
- generic [ref=f1e69]:
- generic [ref=f1e70]: point 1
- generic [ref=f1e71]: captured
- generic [ref=f1e72]:
- generic [ref=f1e73]: point 2
- generic [ref=f1e74]: —
- generic [ref=f1e75]:
- button "capture point 2" [ref=f1e76] [cursor=pointer]
- button "solve transform" [ref=f1e77] [cursor=pointer]
- generic [ref=f1e78]:
- generic [ref=f1e79]:
- generic [ref=f1e80]: ACQUISITION
- generic [ref=f1e81]: ready
- generic [ref=f1e82]:
- generic [ref=f1e83]:
- generic [ref=f1e84]: interval
- slider [ref=f1e85]: "100"
- generic [ref=f1e86]: 120s
- generic [ref=f1e87]:
- generic [ref=f1e88]: timepoints
- slider [ref=f1e89]: "60"
- generic [ref=f1e90]: "60"
- button "start" [ref=f1e92] [cursor=pointer]
- generic [ref=f1e93]:
- generic [ref=f1e94]:
- generic [ref=f1e95]: CURATOR
- generic [ref=f1e96]: live
- generic [ref=f1e97]:
- generic [ref=f1e98]:
- generic [ref=f1e99]: tracking
- generic [ref=f1e100]: e02 · bottom cam · stage
- generic [ref=f1e101]:
- generic [ref=f1e102]: stale
- generic [ref=f1e103]: calibration transform
- generic [ref=f1e104]: Calibration never completed. Acquisition would put e02 off-centre.
- generic [ref=f1e105]:
- button "show me" [active] [ref=f1e106] [cursor=pointer]
- button "dismiss" [ref=f1e107] [cursor=pointer]
- generic [ref=f1e108]: "rule 5: keys 0–5 do this without me"
- generic [ref=f1e109]:
- generic [ref=f1e110]:
- generic [ref=f1e111]: EVENTS
- generic [ref=f1e112]: ready
- generic [ref=f1e113]: no events this session
- generic [ref=f1e115]: everything exists · attention travels · 0–5 · surface zoom ≠ frame zoom
- generic [ref=f1e116]:
- button "0 bench" [ref=f1e117] [cursor=pointer]
- button "1 detect" [ref=f1e118] [cursor=pointer]
- button "2 position" [ref=f1e119] [cursor=pointer]
- button "3 calibrate" [ref=f1e120] [cursor=pointer]
- button "4 acquire" [ref=f1e121] [cursor=pointer]
- button "5 curator" [ref=f1e122] [cursor=pointer]
- generic [ref=f1e123]: 76%
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