Add Cytomat incubator tutorial

docs/user_guide/01_material-handling/_material-handling.rst

@@ -18,5 +18,6 @@ This includes machines for temperature and motion control (as neither machines p
    fans/fans
    temperature
    tilting
+   incubators/cytomat
 
 

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

@@ -0,0 +1 @@
+{"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}