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Use Aravis camera driver instead of PySpin for Cytation#985

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rickwierenga merged 13 commits intoPyLabRobot:v1b1from
vcjdeboer:aravis-pr
Apr 11, 2026
Merged

Use Aravis camera driver instead of PySpin for Cytation#985
rickwierenga merged 13 commits intoPyLabRobot:v1b1from
vcjdeboer:aravis-pr

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@vcjdeboer vcjdeboer commented Apr 3, 2026 •
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Summary

  • Adds an Aravis-based camera driver (AravisCamera) as a drop-in alternative to PySpin for FLIR BlackFly cameras on the Cytation. Eliminates the Spinnaker SDK dependency and the Python 3.10 version cap that PySpin imposes.
  • Splits cytation.py into cytation1.py and cytation5.py — each device creates its own driver internally based on a camera parameter ("aravis" or "pyspin").
  • Adds CytationAravisDriver (connection + optics + camera) and CytationAravisMicroscopyBackend (capture orchestration) following the STARDriver pattern.

New files

File Role
aravis_camera.py Standalone BlackFly driver using Aravis/GenICam via PyGObject
aravis_simulated.py Simulated camera for testing without hardware
cytation_aravis_driver.py Driver layer: BioTekBackend serial + AravisCamera, owns connections and optics
cytation_aravis_microscopy.py MicroscopyBackend: capture orchestration, calls driver methods
cytation1.py Cytation 1 device class (split from cytation.py)
cytation5.py Cytation 5 device class (split from cytation.py)

Modified files

File Change
cytation.py Keeps CytationBackend (PySpin), re-exports device classes for backwards compat
__init__.py Updated exports

Test plan

  • Hardware-tested on Cytation 1 with BlackFly BFLY-U3-13S2M via Aravis on macOS
  • Camera connect/disconnect, exposure, gain, image capture verified
  • Single capture (brightfield 2.5x) and multi-image tiling (2x2) working
  • Filter/objective discovery matches firmware (DAPI, GFP, RFP + objectives)
  • CI: Aravis is an optional dependency (PyGObject + system library) — no import at module level, guarded by HAS_ARAVIS
  • PySpin path unchanged — existing users unaffected

Note: Some CI checks may fail due to pre-existing lint issues on v1b1 (e.g., EL406 unused import) that are not from this PR.

vcjdeboer and others added 6 commits April 5, 2026 09:27
@vcjdeboer @claude
Add Aravis camera driver as PySpin alternative for Cytation
1154357 
Adds a pure-Aravis alternative to PySpin for controlling BlackFly cameras
in the BioTek Cytation. Eliminates the Spinnaker SDK dependency and the
Python 3.10 version cap that PySpin imposes.

New files:
- aravis_camera.py: standalone BlackFly driver using Aravis/GenICam via PyGObject
- aravis_simulated.py: simulated camera for testing without hardware
- cytation_aravis.py: CytationAravisBackend — drop-in replacement for
  CytationBackend using AravisCamera instead of PySpin. Same serial protocol
  for optics (filters, objectives, focus, LED), different camera driver.
  capture() signature matches MicroscopyBackend ABC with backend_params.
- ARAVIS_README.md: installation and usage guide
- test_aravis_connection.ipynb: hardware test notebook

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@vcjdeboer @claude
Remove README and test notebook from aravis PR
f5c3771 
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@vcjdeboer @claude
Split Cytation device classes into separate files, fix Cytation1 bug
cbfd031 
- Move Cytation5 to cytation5.py — takes backend param (PySpin or Aravis)
- Move Cytation1 to cytation1.py — takes backend param, fixes bug where
  BioTekBackend (no capture()) was wired to Microscopy capability
- cytation.py keeps CytationBackend + re-exports devices for backwards compat
- __init__.py updated to import from new files

Both device classes now accept a backend parameter instead of creating
one internally, so users can choose CytationBackend (PySpin) or
CytationAravisBackend (Aravis).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@vcjdeboer @claude
Refactor Aravis backend: split driver/backend, fix camera capture, ha…
b01a373 
…rdware-tested

Architecture refactor following STAR pattern:
- cytation_aravis_driver.py: CytationAravisDriver (BioTekBackend + AravisCamera)
  owns connections, optics control, camera control
- cytation_aravis_microscopy.py: CytationAravisMicroscopyBackend (MicroscopyBackend)
  orchestrates capture by calling driver methods
- cytation1.py/cytation5.py: device classes with camera="aravis"|"pyspin" switch
- Removed monolithic cytation_aravis.py

Bugs fixed during hardware testing:
- aravis_camera.py: trigger() no longer starts/stops acquisition per frame —
  matches PySpin pattern where acquisition brackets the capture loop
- cytation_aravis_driver.py: led_on intensity zfill(3) → zfill(2)
- cytation_aravis_driver.py: _load_filters/_load_objectives use Rick's actual
  firmware protocol (per-slot query) instead of made-up regex parsing
- cytation_aravis_driver.py: all serial commands (set_imaging_mode, set_objective,
  set_focus, select, set_position, led_on/off) now match cytation.py exactly
- cytation_aravis_driver.py: bytes→str decode for firmware responses

Hardware-tested on Cytation 1 with BlackFly BFLY-U3-13S2M:
- Single capture: brightfield 2.5x, real images with correct exposure
- Multi-image tiling: 2x2 grid capture working
- Filter/objective discovery: DAPI, GFP, RFP + 4x PL FL, 2.5x FL Zeiss

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@vcjdeboer @claude
Fix linting and typo check: remove unused imports, fix gir false posi…
86ed38b 
…tive

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude @vcjdeboer
Remove PySpin/Spinnaker dependency, use Aravis exclusively for camera…
5c3b41a 
… access

Replace all PySpin camera code in CytationBackend with AravisCamera calls.
Simplify Cytation1/Cytation5 to always use CytationAravisDriver. Fix
aravis_camera.py to accept serial_number=None (first available camera).
Update docs notebook to use Microscopy.capture(well=...) API.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga rickwierenga changed the title Add Aravis camera driver as PySpin alternative for Cytation Use Aravis camera driver instead of PySpin for Cytation Apr 9, 2026
rickwierenga and others added 3 commits April 9, 2026 16:24
@rickwierenga
Merge remote-tracking branch 'origin/v1b1' into aravis-pr
3b22329 
# Conflicts:
#	docs/user_guide/agilent/biotek/cytation/hello-world.ipynb
#	pylabrobot/agilent/biotek/__init__.py
#	pylabrobot/agilent/biotek/aravis_camera.py
#	pylabrobot/agilent/biotek/cytation.py
@rickwierenga @claude
Consolidate Cytation backends: remove duplicates, port cytation.py lo…
e2e9f99 
…gic to aravis driver

- Remove cytation_aravis.py (duplicate of cytation_aravis_driver.py)
- Remove test_aravis_connection.ipynb (referenced deleted module)
- Port set_imaging_mode version 2 commands from cytation.py to aravis driver
- Port capture orchestration (image_size, tiling, timing) to microscopy backend
- Port acquire_image retry with stop/start recovery to aravis driver
- Add SetupParams to CytationAravisDriver (matches cytation.py pattern)
- Add CaptureParams.overlap to microscopy backend
- Rename CytationAravisMicroscopyBackend -> CytationMicroscopyBackend
- Rename cytation_aravis_microscopy.py -> cytation_microscopy_backend.py

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Refactor Cytation: move all imaging logic to CytationMicroscopyBacken…
8e55d18 
…d, use BioTekBackend directly

- Delete cytation.py (replaced by microscopy backend)
- CytationMicroscopyBackend now owns AravisCamera, camera_serial, imaging_config
- Device classes use BioTekBackend directly as driver (no more CytationAravisDriver)
- use_cam, camera_serial, imaging_config are device-level params passed to backend
- Extract _CytationBase for shared device logic (Cytation1/5)
- Add loading tray capability to both Cytation models
- Filter/objective loading happens in _on_setup
- CytationAravisDriver kept but no longer used by device classes

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
rickwierenga added a commit that referenced this pull request Apr 10, 2026
@rickwierenga @claude
Remove aravis files (moved to separate PR #985)
a4162e5 
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
rickwierenga and others added 4 commits April 9, 2026 17:17
@rickwierenga
Merge remote-tracking branch 'origin/v1b1' into aravis-pr
19bc32c 
# Conflicts:
#	pylabrobot/agilent/biotek/aravis_camera.py
@rickwierenga @claude
Remove dead CytationAravisDriver, fix review issues
812ac89 
- Delete cytation_aravis_driver.py (dead code, duplicated CytationImagingConfig)
- Fix set_gain("machine-auto") to actually enable auto-gain on camera
- Make numpy import optional in aravis_camera.py
- Replace assert with NotImplementedError for overlap check
- Fix CaptureParams docstring (LED intensity is 1-10, not 0-100)
- Fix legacy adapter to use BioTekBackend + CytationMicroscopyBackend directly
- Fix tests to use BioTekBackend directly

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Reorganize biotek/ into plate_readers/ subpackages, fix review issues
f442a1f 
- Move BioTekBackend -> plate_readers/base.py (shared base)
- Move Cytation code -> plate_readers/cytation/ (base, cytation1, cytation5,
  microscopy_backend, aravis_camera)
- Move SynergyH1 -> plate_readers/synergy/
- Update all internal imports, legacy adapters, and docs (rst + notebooks)

Review fixes:
- Wrap led_off() in try/except inside capture() finally so stop_acquisition
  always runs even if the LED command fails
- Restore asyncio.sleep(0.1) stage settle delay in set_position
- Restore max_image_read_attempts default to 50
- Accept backend_params kwarg in CytationMicroscopyBackend._on_setup
- Add PyGObject to cytation-microscopy extra (needed for Aravis)
- Add autofocus example to cytation hello-world notebook

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Update Cytation install instructions for Aravis
c41350b 
Replace Spinnaker SDK / Python 3.10 requirements with Aravis system
library install steps.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga rickwierenga merged commit af69da8 into PyLabRobot:v1b1 Apr 11, 2026
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rickwierenga commented Apr 11, 2026

thanks @vcjdeboer! works super well. very happy to ditch spinnaker

@rickwierenga rickwierenga mentioned this pull request Apr 14, 2026
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@vcjdeboer @rickwierenga