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Remove PySpin/Spinnaker dependency, use Aravis exclusively for camera 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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‎docs/user_guide/agilent/biotek/cytation/hello-world.ipynb‎

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{
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"cell_type": "markdown",
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"id": "wez9bxdabm",
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"source": "# Agilent BioTek Cytation\n\nThe Cytation is an Agilent BioTek multi-mode plate reader with optional microscopy imaging. Depending on the model it supports:\n\n- [Absorbance](../../../capabilities/absorbance)\n- [Fluorescence](../../../capabilities/fluorescence)\n- [Luminescence](../../../capabilities/luminescence)\n- [Microscopy](../../../capabilities/microscopy)\n- [Temperature control](../../../capabilities/temperature-control)\n\n| Model | PLR Name | Plate Reading | Microscopy | Temperature |\n|---|---|---|---|---|\n| Cytation 5 | `Cytation5` | Absorbance, Fluorescence, Luminescence | yes | yes |\n| Cytation 1 | `Cytation1` | -- | yes | yes |\n\nBoth models share the `CytationBackend` driver, which communicates over FTDI USB. The Cytation 5 adds plate-reading capabilities on top of the shared microscopy and temperature-control features.",
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"metadata": {}
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"metadata": {},
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"source": [
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"# Agilent BioTek Cytation\n",
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"\n",
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"The Cytation is an Agilent BioTek multi-mode plate reader with optional microscopy imaging. Depending on the model it supports:\n",
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"\n",
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"- [Absorbance](../../../capabilities/absorbance)\n",
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"- [Fluorescence](../../../capabilities/fluorescence)\n",
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"- [Luminescence](../../../capabilities/luminescence)\n",
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"- [Microscopy](../../../capabilities/microscopy)\n",
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"- [Temperature control](../../../capabilities/temperature-control)\n",
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"\n",
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"| Model | PLR Name | Plate Reading | Microscopy | Temperature |\n",
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"|---|---|---|---|---|\n",
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"| Cytation 5 | `Cytation5` | Absorbance, Fluorescence, Luminescence | yes | yes |\n",
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"| Cytation 1 | `Cytation1` | -- | yes | yes |\n",
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"\n",
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"Both models share the `CytationBackend` driver, which communicates over FTDI USB. The Cytation 5 adds plate-reading capabilities on top of the shared microscopy and temperature-control features."
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]
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},
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{
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"cell_type": "markdown",
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"id": "0rn94ubvq8dj",
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"source": "## Setup\n\nThe examples below use a Cytation 5. For a Cytation 1, replace `Cytation5` with `Cytation1` (the Cytation 1 does not have `.absorbance`, `.fluorescence`, or `.luminescence` attributes).",
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"metadata": {}
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"metadata": {},
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"source": [
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"## Setup\n",
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"\n",
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"The examples below use a Cytation 5. For a Cytation 1, replace `Cytation5` with `Cytation1` (the Cytation 1 does not have `.absorbance`, `.fluorescence`, or `.luminescence` attributes)."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ia4t5ga2ldg",
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"source": "from pylabrobot.agilent.biotek.cytation import Cytation5\n\nc5 = Cytation5(name=\"cytation5\")\nawait c5.setup()",
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"metadata": {},
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"execution_count": null,
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"outputs": []
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"outputs": [],
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"source": [
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"from pylabrobot.agilent.biotek.cytation import Cytation5\n",
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"\n",
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"c5 = Cytation5(name=\"cytation5\")\n",
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"await c5.setup()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "35rmpdivj44",
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"source": "Open and close the tray door. Pass `slow=True` for slower motor travel if needed.",
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"metadata": {}
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"metadata": {},
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"source": [
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"Open and close the tray door. Pass `slow=True` for slower motor travel if needed."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "l85qt1z6hdf",
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"source": "await c5.open()\n\nfrom pylabrobot.resources import Cor_96_wellplate_360ul_Fb\nplate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\nc5.plate_holder.assign_child_resource(plate)\n\nawait c5.close()",
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"metadata": {},
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"execution_count": null,
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"outputs": []
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"outputs": [],
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"source": [
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"await c5.open()\n",
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"\n",
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"from pylabrobot.resources import Cor_96_wellplate_360ul_Fb\n",
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"plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\n",
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"c5.plate_holder.assign_child_resource(plate)\n",
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"\n",
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"await c5.close()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "hxkf2luxk9n",
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"source": "## Plate reading (Cytation 5 only)\n\nThe Cytation 5 exposes `.absorbance`, `.fluorescence`, and `.luminescence` capability objects. For the full API, see [Absorbance](../../../capabilities/absorbance), [Fluorescence](../../../capabilities/fluorescence), and [Luminescence](../../../capabilities/luminescence).",
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"metadata": {}
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"metadata": {},
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"source": [
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"## Plate reading (Cytation 5 only)\n",
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"\n",
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"The Cytation 5 exposes `.absorbance`, `.fluorescence`, and `.luminescence` capability objects. For the full API, see [Absorbance](../../../capabilities/absorbance), [Fluorescence](../../../capabilities/fluorescence), and [Luminescence](../../../capabilities/luminescence)."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "hwipa2rwkzl",
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"source": "# Absorbance\ndata = await c5.absorbance.read_absorbance(wavelength=450)",
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"metadata": {},
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"execution_count": null,
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"outputs": []
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"outputs": [],
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"source": [
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"# Absorbance\n",
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"data = await c5.absorbance.read_absorbance(wavelength=450)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "jmvn8du2t5",
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"source": "# Fluorescence\ndata = await c5.fluorescence.read_fluorescence(\n excitation_wavelength=485, emission_wavelength=528, focal_height=7.5\n)",
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"metadata": {},
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"execution_count": null,
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"outputs": []
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"outputs": [],
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"source": [
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"# Fluorescence\n",
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"data = await c5.fluorescence.read_fluorescence(\n",
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" excitation_wavelength=485, emission_wavelength=528, focal_height=7.5\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "oxn123gjoh",
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"source": "# Luminescence\ndata = await c5.luminescence.read_luminescence(focal_height=4.5)",
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"metadata": {},
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"execution_count": null,
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"outputs": []
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"outputs": [],
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"source": [
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"# Luminescence\n",
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"data = await c5.luminescence.read_luminescence(focal_height=4.5)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "1qn3t2pqvw",
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"source": "## Microscopy\n\nBoth the Cytation 5 and Cytation 1 expose a `.microscopy` capability. For imaging, pass `use_cam=True` during setup so the Spinnaker camera is initialized. For the full API, see [Microscopy](../../../capabilities/microscopy).\n\nUse {class}`~pylabrobot.agilent.biotek.cytation.CytationBackend.CaptureParams` to control LED intensity, coverage tiling, and pixel format.",
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"metadata": {}
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"metadata": {},
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"source": [
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"## Microscopy\n",
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"\n",
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"Both the Cytation 5 and Cytation 1 expose a `.microscopy` capability. For imaging, pass `use_cam=True` during setup so the Spinnaker camera is initialized. For the full API, see [Microscopy](../../../capabilities/microscopy).\n",
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"\n",
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"Use {class}`~pylabrobot.agilent.biotek.cytation.CytationBackend.CaptureParams` to control LED intensity, coverage tiling, and pixel format."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "qr1jm6691a",
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"source": "from pylabrobot.agilent.biotek.cytation import CytationBackend, CytationImagingConfig\nfrom pylabrobot.capabilities.microscopy.standard import ImagingMode, Objective\n\nres = await c5.microscopy.capture(\n row=1,\n column=2,\n mode=ImagingMode.BRIGHTFIELD,\n objective=Objective.O_4X_PL_FL_Phase,\n focal_height=0.833,\n exposure_time=5,\n gain=16,\n plate=plate,\n backend_params=CytationBackend.CaptureParams(led_intensity=10),\n)",
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"metadata": {},
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"outputs": [],
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"source": [
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"from pylabrobot.agilent.biotek.cytation import CytationBackend, CytationImagingConfig\n",
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"from pylabrobot.capabilities.microscopy.standard import ImagingMode, Objective\n",
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"\n",
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"res = await c5.microscopy.capture(\n",
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" well=(1, 2),\n",
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" mode=ImagingMode.BRIGHTFIELD,\n",
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" objective=Objective.O_4X_PL_FL_Phase,\n",
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" focal_height=0.833,\n",
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" exposure_time=5,\n",
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" gain=16,\n",
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" plate=plate,\n",
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" backend_params=CytationBackend.CaptureParams(led_intensity=10),\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"outputs": []
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"id": "b7125e49",
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"metadata": {},
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"outputs": [],
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"source": [
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"from PIL import Image\n",
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"img = Image.fromarray(res.images[0])\n",
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"img"
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]
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},
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{
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"cell_type": "markdown",
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"id": "km95iou30f",
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"source": "Tile multiple fields of view with the `coverage` parameter:",
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"metadata": {}
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"metadata": {},
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"source": [
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"Tile multiple fields of view with the `coverage` parameter:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "fi1o94l1uni",
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"source": "res = await c5.microscopy.capture(\n row=1,\n column=2,\n mode=ImagingMode.BRIGHTFIELD,\n objective=Objective.O_4X_PL_FL_Phase,\n focal_height=0.833,\n exposure_time=5,\n gain=16,\n plate=plate,\n backend_params=CytationBackend.CaptureParams(\n led_intensity=10,\n coverage=(4, 4),\n ),\n)\nprint(f\"{len(res.images)} images captured\")",
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"metadata": {},
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"execution_count": null,
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"outputs": []
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"outputs": [],
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"source": [
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"res = await c5.microscopy.capture(\n",
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" well=(1, 2),\n",
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" mode=ImagingMode.BRIGHTFIELD,\n",
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" objective=Objective.O_4X_PL_FL_Phase,\n",
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" focal_height=0.833,\n",
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" exposure_time=5,\n",
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" gain=16,\n",
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" plate=plate,\n",
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" backend_params=CytationBackend.CaptureParams(\n",
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" led_intensity=10,\n",
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" coverage=(4, 4),\n",
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" ),\n",
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")\n",
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"print(f\"{len(res.images)} images captured\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "sa9pdeeo51",
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"source": "## Temperature control\n\nBoth models expose a `.temperature` controller. For the full API, see [Temperature Control](../../../capabilities/temperature-control).",
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"metadata": {}
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"metadata": {},
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"source": [
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"## Temperature control\n",
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"\n",
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"Both models expose a `.temperature` controller. For the full API, see [Temperature Control](../../../capabilities/temperature-control)."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "qhsjnerhl3",
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"source": "await c5.temperature.set_temperature(37.0)\n\ncurrent = await c5.temperature.request_temperature()\nprint(f\"{current:.1f} \\u00b0C\")\n\nawait c5.temperature.deactivate()",
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"metadata": {},
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"execution_count": null,
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"outputs": []
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"outputs": [],
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"source": [
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"await c5.temperature.set_temperature(37.0)\n",
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"\n",
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"current = await c5.temperature.request_temperature()\n",
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"print(f\"{current:.1f} \\u00b0C\")\n",
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"\n",
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"await c5.temperature.deactivate()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "f667qnt4occ",
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"source": "## Teardown",
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"metadata": {}
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"metadata": {},
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"source": [
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"## Teardown"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "xcqz2zwu04g",
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"source": "await c5.stop()",
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"metadata": {},
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"execution_count": null,
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"outputs": []
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"outputs": [],
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"source": [
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"await c5.stop()"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "env",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"version": "3.11.0"
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.15"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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}

‎pylabrobot/agilent/__init__.py‎

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from .biotek import (
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EL406,
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AravisImagingConfig,
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BioTekBackend,
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Cytation1,
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Cytation5,
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CytationAravisDriver,
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CytationBackend,
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CytationImagingConfig,
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EL406Driver,

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