Add Aravis camera driver as PySpin alternative for Cytation

docs/user_guide/agilent/biotek/cytation/hello-world.ipynb

@@ -3,135 +3,258 @@
   {
    "cell_type": "markdown",
    "id": "wez9bxdabm",
-   "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.",
-   "metadata": {}
+   "metadata": {},
+   "source": [
+    "# Agilent BioTek Cytation\n",
+    "\n",
+    "The 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",
+    "\n",
+    "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."
+   ]
   },
   {
    "cell_type": "markdown",
    "id": "0rn94ubvq8dj",
-   "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).",
-   "metadata": {}
+   "metadata": {},
+   "source": [
+    "## Setup\n",
+    "\n",
+    "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)."
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
    "id": "ia4t5ga2ldg",
-   "source": "from pylabrobot.agilent.biotek.cytation import Cytation5\n\nc5 = Cytation5(name=\"cytation5\")\nawait c5.setup()",
    "metadata": {},
-   "execution_count": null,
-   "outputs": []
+   "outputs": [],
+   "source": [
+    "from pylabrobot.agilent.biotek.cytation import Cytation5\n",
+    "\n",
+    "c5 = Cytation5(name=\"cytation5\")\n",
+    "await c5.setup()"
+   ]
   },
   {
    "cell_type": "markdown",
    "id": "35rmpdivj44",
-   "source": "Open and close the tray door. Pass `slow=True` for slower motor travel if needed.",
-   "metadata": {}
+   "metadata": {},
+   "source": [
+    "Open and close the tray door. Pass `slow=True` for slower motor travel if needed."
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
    "id": "l85qt1z6hdf",
-   "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()",
    "metadata": {},
-   "execution_count": null,
-   "outputs": []
+   "outputs": [],
+   "source": [
+    "await c5.open()\n",
+    "\n",
+    "from pylabrobot.resources import Cor_96_wellplate_360ul_Fb\n",
+    "plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\n",
+    "c5.plate_holder.assign_child_resource(plate)\n",
+    "\n",
+    "await c5.close()"
+   ]
   },
   {
    "cell_type": "markdown",
    "id": "hxkf2luxk9n",
-   "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).",
-   "metadata": {}
+   "metadata": {},
+   "source": [
+    "## Plate reading (Cytation 5 only)\n",
+    "\n",
+    "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)."
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
    "id": "hwipa2rwkzl",
-   "source": "# Absorbance\ndata = await c5.absorbance.read_absorbance(wavelength=450)",
    "metadata": {},
-   "execution_count": null,
-   "outputs": []
+   "outputs": [],
+   "source": [
+    "# Absorbance\n",
+    "data = await c5.absorbance.read_absorbance(wavelength=450)"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
    "id": "jmvn8du2t5",
-   "source": "# Fluorescence\ndata = await c5.fluorescence.read_fluorescence(\n    excitation_wavelength=485, emission_wavelength=528, focal_height=7.5\n)",
    "metadata": {},
-   "execution_count": null,
-   "outputs": []
+   "outputs": [],
+   "source": [
+    "# Fluorescence\n",
+    "data = await c5.fluorescence.read_fluorescence(\n",
+    "    excitation_wavelength=485, emission_wavelength=528, focal_height=7.5\n",
+    ")"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
    "id": "oxn123gjoh",
-   "source": "# Luminescence\ndata = await c5.luminescence.read_luminescence(focal_height=4.5)",
    "metadata": {},
-   "execution_count": null,
-   "outputs": []
+   "outputs": [],
+   "source": [
+    "# Luminescence\n",
+    "data = await c5.luminescence.read_luminescence(focal_height=4.5)"
+   ]
   },
   {
    "cell_type": "markdown",
    "id": "1qn3t2pqvw",
-   "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.",
-   "metadata": {}
+   "metadata": {},
+   "source": [
+    "## Microscopy\n",
+    "\n",
+    "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",
+    "\n",
+    "Use {class}`~pylabrobot.agilent.biotek.cytation.CytationBackend.CaptureParams` to control LED intensity, coverage tiling, and pixel format."
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
    "id": "qr1jm6691a",
-   "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)",
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pylabrobot.agilent.biotek.cytation import CytationBackend, CytationImagingConfig\n",
+    "from pylabrobot.capabilities.microscopy.standard import ImagingMode, Objective\n",
+    "\n",
+    "res = await c5.microscopy.capture(\n",
+    "    well=(1, 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",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
    "execution_count": null,
-   "outputs": []
+   "id": "b7125e49",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from PIL import Image\n",
+    "img = Image.fromarray(res.images[0])\n",
+    "img"
+   ]
   },
   {
    "cell_type": "markdown",
    "id": "km95iou30f",
-   "source": "Tile multiple fields of view with the `coverage` parameter:",
-   "metadata": {}
+   "metadata": {},
+   "source": [
+    "Tile multiple fields of view with the `coverage` parameter:"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
    "id": "fi1o94l1uni",
-   "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\")",
    "metadata": {},
-   "execution_count": null,
-   "outputs": []
+   "outputs": [],
+   "source": [
+    "res = await c5.microscopy.capture(\n",
+    "    well=(1, 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",
+    ")\n",
+    "print(f\"{len(res.images)} images captured\")"
+   ]
   },
   {
    "cell_type": "markdown",
    "id": "sa9pdeeo51",
-   "source": "## Temperature control\n\nBoth models expose a `.temperature` controller. For the full API, see [Temperature Control](../../../capabilities/temperature-control).",
-   "metadata": {}
+   "metadata": {},
+   "source": [
+    "## Temperature control\n",
+    "\n",
+    "Both models expose a `.temperature` controller. For the full API, see [Temperature Control](../../../capabilities/temperature-control)."
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
    "id": "qhsjnerhl3",
-   "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()",
    "metadata": {},
-   "execution_count": null,
-   "outputs": []
+   "outputs": [],
+   "source": [
+    "await c5.temperature.set_temperature(37.0)\n",
+    "\n",
+    "current = await c5.temperature.request_temperature()\n",
+    "print(f\"{current:.1f} \\u00b0C\")\n",
+    "\n",
+    "await c5.temperature.deactivate()"
+   ]
   },
   {
    "cell_type": "markdown",
    "id": "f667qnt4occ",
-   "source": "## Teardown",
-   "metadata": {}
+   "metadata": {},
+   "source": [
+    "## Teardown"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
    "id": "xcqz2zwu04g",
-   "source": "await c5.stop()",
    "metadata": {},
-   "execution_count": null,
-   "outputs": []
+   "outputs": [],
+   "source": [
+    "await c5.stop()"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "env",
    "language": "python",
    "name": "python3"
   },
   "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
    "name": "python",
-   "version": "3.11.0"
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.15"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

pylabrobot/agilent/__init__.py

@@ -1,8 +1,10 @@
 from .biotek import (
   EL406,
+  AravisImagingConfig,
   BioTekBackend,
   Cytation1,
   Cytation5,
+  CytationAravisDriver,
   CytationBackend,
   CytationImagingConfig,
   EL406Driver,

pylabrobot/agilent/biotek/__init__.py

@@ -1,9 +1,7 @@
 from .biotek import BioTekBackend
-from .cytation import (
-  Cytation1,
-  Cytation5,
-  CytationBackend,
-  CytationImagingConfig,
-)
+from .cytation import CytationBackend, CytationImagingConfig
+from .cytation1 import Cytation1
+from .cytation5 import Cytation5
+from .cytation_aravis_driver import AravisImagingConfig, CytationAravisDriver
 from .el406 import EL406, EL406Driver, EL406PlateWashingBackend, EL406ShakingBackend
 from .synergy_h1 import SynergyH1, SynergyH1Backend