Add Aravis camera driver as PySpin alternative for Cytation#985
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vcjdeboer wants to merge 6 commits intoPyLabRobot:v1b1from
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Add Aravis camera driver as PySpin alternative for Cytation#985vcjdeboer wants to merge 6 commits intoPyLabRobot:v1b1from
vcjdeboer wants to merge 6 commits intoPyLabRobot:v1b1from
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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>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- 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>
…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>
…tive Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
… 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>
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Summary
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.cytation.pyintocytation1.pyandcytation5.py— each device creates its own driver internally based on acameraparameter ("aravis"or"pyspin").CytationAravisDriver(connection + optics + camera) andCytationAravisMicroscopyBackend(capture orchestration) following the STARDriver pattern.New files
aravis_camera.pyaravis_simulated.pycytation_aravis_driver.pycytation_aravis_microscopy.pycytation1.pycytation5.pyModified files
cytation.py__init__.pyTest plan
HAS_ARAVISNote: Some CI checks may fail due to pre-existing lint issues on v1b1 (e.g., EL406 unused import) that are not from this PR.