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Docs Update: add placeholder notebook for BMG Labtech CLARIOstar (#660)
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‎docs/user_guide/02_analytical/plate-reading/bmg-clariostar.ipynb‎

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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": "18708b66",
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"metadata": {},
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"source": [
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"# BMG Labtech CLARIOstar (Plus)\n",
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"\n",
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"| Summary | Photo |\n",
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"|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------|\n",
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"| - [OEM Link](https://www.bmglabtech.com/en/clariostar-plus/)<br>- **Communication Protocol / Hardware**: Serial (FTDI)/ USB-A<br>- **Communication Level**: Firmware<br>- **Measurement Modes**: Absorbance, Luminescence, Fluorescence <br>- **Plate Delivery**: Loading tray<br>- **Additional Standard Features**: Temperature sontrol, Shaking<br><br>- **Additional Upgrades**: Injector system, increased max temperature, plate stacking system, ... | ![quadrants](img/bmg-labtech-clariostar-plus.png) |\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": "80e2e5dc",
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"metadata": {},
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"source": [
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"---\n",
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"## Setup Instructions (Physical)\n",
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"\n",
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"The CLARIOstar and CLARIOstar Plus require a minimum of two cable connections to be operational:\n",
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"1. Power cord (standard IEC C13)\n",
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"2. USB cable (USB-B with security screws at CLARIOstar end; USB-A at control PC end)\n",
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"\n",
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"Optional:\n",
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"If you have a plate stacking unit to use with the CLARIOstar (Plus), an additional RS-232 port is available on the CLARIOstar (Plus).\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": "adb29364",
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"metadata": {},
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"source": [
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"---\n",
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"## Setup Instructions (Programmatic)\n",
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"\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": "34531f2c",
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"metadata": {},
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"outputs": [],
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"source": [
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"%load_ext autoreload\n",
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"%autoreload 2"
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]
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},
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{
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"cell_type": "markdown",
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"id": "e7a179e9",
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"metadata": {},
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"source": [
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"To control the BMG Labtech CLARIOstar (Plus), generate a `PlateReader` frontend instance that uses a `CLARIOstarBackend` instance as its backend.\n",
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"\n",
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"To access the CLARIOstar-specific machine features you can still use the backend directly.\n",
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"For convenience, it is useful to therefore store the backend instance as a separate `clariostar_backend` variable."
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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": "363b8144",
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"metadata": {},
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"outputs": [],
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"source": [
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"from pylabrobot.plate_reading import PlateReader\n",
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"\n",
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"from pylabrobot.plate_reading.clario_star_backend import CLARIOstarBackend\n",
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"clariostar_backend = CLARIOstarBackend()\n",
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"\n",
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"pr = PlateReader(\n",
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" name=\"CLARIOstar\",\n",
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" backend=clariostar_backend,\n",
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" size_x=0.0, # TODO: generate new handling for resources with loading tray \n",
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" size_y=0.0,\n",
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" size_z=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": "code",
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"execution_count": null,
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"id": "30720acb",
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"metadata": {},
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"outputs": [],
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"source": [
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"await pr.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": "65555028",
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"metadata": {},
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"source": [
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"```{note}\n",
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"Expected behaviour: the machine should perform its initialization routine.\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": "7d2e9ed2",
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"metadata": {},
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"source": [
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"---\n",
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"\n",
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"## Usage / Machine Features\n",
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"\n",
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"### 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": "c0834a6e",
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"metadata": {},
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"outputs": [],
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"source": [
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"await pr.open()"
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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": 2,
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"id": "77c3406b",
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"metadata": {},
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"outputs": [],
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"source": [
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"# perform arm movement to move your plate of interest onto the CLARIOstar's loading tray\n",
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"# this movement can be performed by a human\n",
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"# or it can be performed by a robotic arm"
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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": "092a02fa",
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"metadata": {},
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"outputs": [],
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"source": [
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"await pr.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": "9c4d21b7",
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"metadata": {},
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"source": [
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"### Set Temperature\n",
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"\n",
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"The CLARIOstar offers a temperature control feature.\n",
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"Reaching a set temperature is relatively slow compared to standalone temperature controllers.\n",
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"We therefore recommend setting the temperature early on in your automated Protocol (aP)."
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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": 3,
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"id": "bb2de16b",
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"metadata": {},
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"outputs": [],
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"source": [
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"# WIP: feature exposure in active development"
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]
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},
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{
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"cell_type": "markdown",
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"id": "bf4840ea",
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"metadata": {},
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"source": [
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"### Set Shaking\n",
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"\n",
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"The CLARIOstar offers a shaking feature."
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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": "60b71bea",
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"metadata": {},
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"outputs": [],
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"source": [
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"# WIP: feature in active development"
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]
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},
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{
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"cell_type": "markdown",
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"id": "c4be6218",
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"metadata": {},
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"source": [
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"---\n",
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"### Measuring Absorbance\n",
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"\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": "e23acc3d",
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"metadata": {},
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"outputs": [],
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"source": [
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"# WIP: feature in active development including\n",
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"# reading subsets of wells\n",
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"# specifying orbital diameter\n",
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"# specifying number of technical replicate measurements per well\n",
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"# specifying start position for reading: topleft, topright, bottomleft, bottomright\n",
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"# ...\n",
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"\n",
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"results_absorbance = await pr.read_absorbance()\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": "d9a13de2",
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"metadata": {},
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"source": [
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"`results` will be a width x height array of absorbance values.\n",
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"\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": "e57e55de",
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"metadata": {},
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"source": [
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"\n",
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"#### Performing a Spectral Scan\n",
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"\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": "8cae50a6",
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"metadata": {},
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"outputs": [],
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"source": [
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"# WIP: feature in active development"
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]
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},
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{
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"cell_type": "markdown",
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"id": "c7a70d7e",
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"metadata": {},
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"source": [
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"### Measuring Luminescence\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": "c8656ef6",
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"metadata": {},
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"outputs": [],
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"source": [
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"# WIP: feature in active development\n",
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"\n",
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"results_luminescence = await pr.read_luminescence()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "8554a66c",
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"metadata": {},
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"source": [
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"### Measuring Fluorescence\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": "637f06a7",
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"metadata": {},
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"outputs": [],
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"source": [
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"# WIP: feature in active development"
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]
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},
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{
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"cell_type": "markdown",
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"id": "362dd696",
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"metadata": {},
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"source": [
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"### Using the Injector Needles\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": "cd676c58",
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"metadata": {},
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"outputs": [],
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"source": [
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"# WIP: feature in active development"
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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": "plr",
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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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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.11"
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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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}

‎docs/user_guide/02_analytical/plate-reading/bmg-clariostar.rst‎

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‎docs/user_guide/02_analytical/plate-reading/img/bmg-labtech-clariostar-plus.png‎

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‎docs/user_guide/02_analytical/plate-reading/plate-reading.rst‎

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PyLabRobot supports the following plate readers:
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- :ref:`BMG Clariostar <clariostar>`
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- `BMG Labtech CLARIOstar`
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Plate readers are controlled by the :class:`~pylabrobot.plate_reading.plate_reader.PlateReader` class. This class takes a backend as an argument. The backend is responsible for communicating with the plate reader and is specific to the hardware being used.
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.. toctree::

‎docs/user_guide/machines.md‎

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| Manufacturer | Machine | Features | PLR-Support | Links |
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|--------------|---------|----------|-------------|--------|
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| BMG Labtech | CLARIOstar | <span class="badge badge-absorbance">absorbance</span><span class="badge badge-fluorescence">fluorescence</span><span class="badge badge-luminescence">luminescence</span> | Full | [PLR](https://docs.pylabrobot.org/user_guide/02_analytical/plate-reading/bmg-clariostar.html) / [OEM](https://www.bmglabtech.com/en/clariostar-plus/) |
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| BMG Labtech | CLARIOstar (Plus) | <span class="badge badge-absorbance">absorbance</span><span class="badge badge-fluorescence">fluorescence</span><span class="badge badge-luminescence">luminescence</span> | Full | [PLR](https://docs.pylabrobot.org/user_guide/02_analytical/plate-reading/bmg-clariostar.html) / [OEM](https://www.bmglabtech.com/en/clariostar-plus/) |
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| Agilent (BioTek) | Cytation 1 | <span class="badge badge-absorbance">absorbance</span><span class="badge badge-fluorescence">fluorescence</span><span class="badge badge-luminescence">luminescence</span><span class="badge badge-microscopy">microscopy</span> | Full | [PLR](https://docs.pylabrobot.org/user_guide/02_analytical/plate-reading/cytation5.html) / [OEM](https://www.agilent.com/en/product/cell-analysis/cell-imaging-microscopy/cell-imaging-multimode-readers/biotek-cytation-1-cell-imaging-multimode-reader-1623200) |
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| Agilent (BioTek) | Cytation 5 | <span class="badge badge-absorbance">absorbance</span><span class="badge badge-fluorescence">fluorescence</span><span class="badge badge-luminescence">luminescence</span><span class="badge badge-microscopy">microscopy</span> | Full | [PLR](https://docs.pylabrobot.org/user_guide/02_analytical/plate-reading/cytation5.html) / [OEM](https://www.agilent.com/en/product/cell-analysis/cell-imaging-microscopy/cell-imaging-multimode-readers/biotek-cytation-5-cell-imaging-multimode-reader-1623202) |
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| Byonoy | Absorbance 96 Automate | <span class="badge badge-absorbance">absorbance</span> | WIP | [OEM](https://byonoy.com/absorbance-96-automate/) |

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