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