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 "cells": [
  {
   "cell_type": "markdown",
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   "source": [
    "# ImageXpress Pico\n",
    "\n",
    "The [Molecular Devices ImageXpress Pico](https://www.moleculardevices.com/products/cellular-imaging-systems/high-content-imaging/imagexpress-pico) is an automated cell imaging system. PyLabRobot communicates with it over SiLA 2 / gRPC.\n",
    "\n",
    "## Requirements\n",
    "\n",
    "- The Pico must be running the SiLA 2 server (default port 8091).\n",
    "- `pip install grpcio numpy Pillow`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.plate_reading import Imager, ImagingMode, Objective\n",
    "from pylabrobot.microscopes.molecular_devices.pico.backend import ExperimentalPicoBackend"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create the backend, specifying which objectives and filter cubes are physically installed on your instrument. The keys are 0-indexed turret / filter-wheel positions."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "backend = ExperimentalPicoBackend(\n",
    "  host=\"192.168.1.100\",\n",
    "  objectives={0: Objective.O_4X_PL_FL},\n",
    "  filter_cubes={0: ImagingMode.DAPI, 1: ImagingMode.BRIGHTFIELD},\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pico = Imager(name=\"pico\", size_x=0, size_y=0, size_z=0, backend=backend)\n",
    "await pico.setup()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Assign a plate\n",
    "\n",
    "The plate geometry is used to derive the labware parameters sent to the Pico. Any PLR `Plate` definition works."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.resources import CellVis_96_wellplate_350uL_Fb\n",
    "\n",
    "plate = CellVis_96_wellplate_350uL_Fb(name=\"plate\")\n",
    "pico.assign_child_resource(plate)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Loading a plate\n",
    "\n",
    "Open the plate drawer, place the plate, and close it."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await pico.backend.open_door()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Place the plate in the drawer, then close it.\n",
    "await pico.backend.close_door()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Capture an image\n",
    "\n",
    "Supported objectives:\n",
    "\n",
    "- `O_2_5X_N_PLAN` — N PLAN 2.5x/0.07\n",
    "- `O_4X_PL_FL` — PL FLUOTAR 4x/0.13\n",
    "- `O_10X_PL_FL` — PL FLUOTAR 10x/0.30\n",
    "- `O_20X_PL_FL` — PL FLUOTAR 20x/0.40\n",
    "- `O_40X_PL_FL` — PL FLUOTAR 40x/0.60\n",
    "\n",
    "Supported imaging modes:\n",
    "\n",
    "- `BRIGHTFIELD`\n",
    "- `DAPI`\n",
    "- `GFP`\n",
    "- `RFP`\n",
    "- `TEXAS_RED`\n",
    "- `CY5`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "res = await pico.capture(\n",
    "  well=(0, 0),  # A1\n",
    "  mode=ImagingMode.BRIGHTFIELD,\n",
    "  objective=Objective.O_4X_PL_FL,\n",
    "  exposure_time=10.0,  # ms\n",
    "  focal_height=1.0,    # mm\n",
    "  gain=0,\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "\n",
    "plt.imshow(res.images[0], cmap=\"gray\")\n",
    "plt.title(f\"Exposure: {res.exposure_time:.1f} ms\")\n",
    "plt.axis(\"off\")\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You can also pass a `Well` object directly:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "res = await pico.capture(\n",
    "  well=plate.get_well(\"B3\"),\n",
    "  mode=ImagingMode.DAPI,\n",
    "  objective=Objective.O_4X_PL_FL,\n",
    "  exposure_time=15.0,\n",
    "  focal_height=1.0,\n",
    "  gain=0,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Cleanup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await pico.stop()"
   ]
  }
 ],
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