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fix cytomat notebook
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‎docs/user_guide/01_material-handling/incubators/cytomat.ipynb‎

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{"cells": [{"cell_type": "markdown", "id": "abb22091", "metadata": {}, "source": ["# Hello World, \"Cytomat Incubator\"!\n", "\n", "The Cytomat series of incubators is used for storing microplates under\n", "controlled environmental conditions. PyLabRobot implements the\n", "{class}`~pylabrobot.incubators.cytomat.cytomat.CytomatBackend` which\n", "supports several models such as `C6000`, `C6002`, `C2C_50`, `C2C_425`,\n", "`C2C_450_SHAKE` and `C5C`.\n", "\n", "In this tutorial we show how to:\n", "- connect to the incubator\n", "- configure racks\n", "- move plates in and out\n", "- monitor temperature and humidity\n", "\n", "```{note}\n", "This notebook uses `await` statements which must be run inside an\n", "asynchronous environment such as `asyncio`.\n", "```"]}, {"cell_type": "code", "execution_count": null, "id": "b6b9218a", "metadata": {}, "outputs": [], "source": ["from pylabrobot.incubators import CytomatBackend, CytomatType\n", "from pylabrobot.incubators.cytomat.racks import cytomat_rack_9mm_51\n", "from pylabrobot.incubators.incubator import Incubator\n", "from pylabrobot.resources.corning.plates import Cor_96_wellplate_360ul_Fb\n", "from pylabrobot.resources import Coordinate\n", "\n", "# Connect to the incubator via a serial port\n", "backend = CytomatBackend(model=CytomatType.C6000, port=\"/dev/ttyUSB0\")\n", "\n", "# Create a rack and assemble an `Incubator` resource\n", "rack = cytomat_rack_9mm_51(\"rack_A\")\n", "incubator = Incubator(\n", " backend=backend,\n", " name=\"cyto\",\n", " size_x=860,\n", " size_y=550,\n", " size_z=900,\n", " racks=[rack],\n", " loading_tray_location=Coordinate(0, 0, 0),\n", ")"]}, {"cell_type": "markdown", "id": "de3fe5c6", "metadata": {}, "source": ["## Setup\n", "\n", "Setting up the incubator opens the serial connection and initializes the\n", "device."]}, {"cell_type": "code", "execution_count": null, "id": "cee39594", "metadata": {}, "outputs": [], "source": ["await incubator.setup()"]}, {"cell_type": "markdown", "id": "8f379ea7", "metadata": {}, "source": ["## Storing a plate\n", "\n", "To store a plate we first place it on the loading tray and then call\n", "{meth}`~pylabrobot.incubators.incubator.Incubator.take_in_plate`.\n", "You can choose a site automatically or specify one explicitly.\n"]}, {"cell_type": "code", "execution_count": null, "id": "25169f81", "metadata": {}, "outputs": [], "source": ["plate = Cor_96_wellplate_360ul_Fb(\"my_plate\")\n", "incubator.loading_tray.assign_child_resource(plate)\n", "await incubator.take_in_plate(\"smallest\") # choose the smallest free site\n", "\n", "# other options:\n", "# await incubator.take_in_plate(\"random\") # random free site\n", "# await incubator.take_in_plate(rack[3]) # store at rack position 3\n"]}, {"cell_type": "markdown", "id": "31f1c241", "metadata": {}, "source": ["## Retrieving a plate\n", "\n", "Use {meth}`~pylabrobot.incubators.incubator.Incubator.fetch_plate_to_loading_tray`\n", "to move a plate from storage to the loading tray."]}, {"cell_type": "code", "execution_count": null, "id": "632ec3f7", "metadata": {}, "outputs": [], "source": ["await incubator.fetch_plate_to_loading_tray(\"my_plate\")\n", "retrieved = incubator.loading_tray.resource"]}, {"cell_type": "markdown", "id": "7dc4dfb9", "metadata": {}, "source": ["## Monitoring conditions\n", "\n", "The Cytomat provides queries for temperature and humidity."]}, {"cell_type": "code", "execution_count": null, "id": "0d768495", "metadata": {}, "outputs": [], "source": ["current_temp = await incubator.get_temperature()\n", "current_humidity = await incubator.backend.get_humidity()\n", "print(current_temp, current_humidity)"]}, {"cell_type": "markdown", "id": "7c27b01e", "metadata": {}, "source": ["## Shutdown\n", "\n", "Always close the connection when finished."]}, {"cell_type": "code", "execution_count": null, "id": "28b68d42", "metadata": {}, "outputs": [], "source": ["await incubator.stop()"]}], "metadata": {"jupytext": {"cell_metadata_filter": "-all", "main_language": "python", "notebook_metadata_filter": "-all"}}, "nbformat": 4, "nbformat_minor": 5}
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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "abb22091",
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"metadata": {},
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"source": [
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"# Hello World, \"Cytomat Incubator\"!\n",
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"\n",
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"The Cytomat series of incubators is used for storing microplates under\n",
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"controlled environmental conditions. PyLabRobot implements the\n",
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"{class}`~pylabrobot.incubators.cytomat.cytomat.CytomatBackend` which\n",
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"supports several models such as `C6000`, `C6002`, `C2C_50`, `C2C_425`,\n",
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"`C2C_450_SHAKE` and `C5C`.\n",
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"\n",
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"In this tutorial we show how to:\n",
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"- connect to the incubator\n",
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"- configure racks\n",
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"- move plates in and out\n",
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"- monitor temperature and humidity\n",
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"\n",
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"```{note}\n",
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"This notebook uses `await` statements which must be run inside an\n",
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"asynchronous environment such as `asyncio`.\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": "b6b9218a",
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"metadata": {},
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"outputs": [],
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"source": [
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"from pylabrobot.incubators import CytomatBackend, CytomatType\n",
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"from pylabrobot.incubators.cytomat.racks import cytomat_rack_9mm_51\n",
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"from pylabrobot.incubators.incubator import Incubator\n",
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"from pylabrobot.resources.corning.plates import Cor_96_wellplate_360ul_Fb\n",
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"from pylabrobot.resources import Coordinate\n",
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"\n",
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"# Connect to the incubator via a serial port\n",
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"backend = CytomatBackend(model=CytomatType.C6000, port=\"/dev/ttyUSB0\")\n",
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"\n",
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"# Create a rack and assemble an `Incubator` resource\n",
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"rack = cytomat_rack_9mm_51(\"rack_A\")\n",
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"incubator = Incubator(\n",
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" backend=backend,\n",
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" name=\"cyto\",\n",
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" size_x=860,\n",
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" size_y=550,\n",
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" size_z=900,\n",
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" racks=[rack],\n",
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" loading_tray_location=Coordinate(0, 0, 0),\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "de3fe5c6",
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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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"Setting up the incubator opens the serial connection and initializes the\n",
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"device."
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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": "cee39594",
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"metadata": {},
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"outputs": [],
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"source": [
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"await incubator.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": "8f379ea7",
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"metadata": {},
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"source": [
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"## Storing a plate\n",
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"\n",
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"To store a plate we first place it on the loading tray and then call\n",
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"{meth}`~pylabrobot.incubators.incubator.Incubator.take_in_plate`.\n",
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"You can choose a site automatically or specify one explicitly.\n"
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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": "25169f81",
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"metadata": {},
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"outputs": [],
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"source": [
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"plate = Cor_96_wellplate_360ul_Fb(\"my_plate\")\n",
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"incubator.loading_tray.assign_child_resource(plate)\n",
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"await incubator.take_in_plate(\"smallest\") # choose the smallest free site\n",
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"\n",
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"# other options:\n",
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"# await incubator.take_in_plate(\"random\") # random free site\n",
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"# await incubator.take_in_plate(rack[3]) # store at rack position 3\n"
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]
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},
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{
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"cell_type": "markdown",
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"id": "31f1c241",
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"metadata": {},
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"source": [
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"## Retrieving a plate\n",
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"\n",
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"Use {meth}`~pylabrobot.incubators.incubator.Incubator.fetch_plate_to_loading_tray`\n",
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"to move a plate from storage to the loading tray."
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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": "632ec3f7",
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"metadata": {},
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"outputs": [],
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"source": [
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"await incubator.fetch_plate_to_loading_tray(\"my_plate\")\n",
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"retrieved = incubator.loading_tray.resource"
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]
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},
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{
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"cell_type": "markdown",
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"id": "7dc4dfb9",
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"metadata": {},
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"source": [
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"## Monitoring conditions\n",
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"\n",
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"The Cytomat provides queries for temperature and humidity."
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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": "0d768495",
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"metadata": {},
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"outputs": [],
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"source": [
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"current_temp = await incubator.get_temperature()\n",
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"current_humidity = await incubator.backend.get_humidity()\n",
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"print(current_temp, current_humidity)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "7c27b01e",
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"metadata": {},
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"source": [
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"## Shutdown\n",
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"\n",
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"Always close the connection when finished."
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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": "28b68d42",
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"metadata": {},
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"outputs": [],
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"source": [
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"await incubator.stop()"
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]
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}
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],
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"metadata": {
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"jupytext": {
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"cell_metadata_filter": "-all",
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"main_language": "python",
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"notebook_metadata_filter": "-all"
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},
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"language_info": {
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"name": "python"
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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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