feat: add barseq instrument (#1685)

* feat: add barseq instrument

* refactor: SlapPlane -> Slap2Plane

* Revert "refactor: SlapPlane -> Slap2Plane"

This reverts commit 6f193b8.

* chore: lint

* refactor: fix serialization code in example

* fix: fix issues blocking build

* chore: fix write function for instrument example

Author: dbirman

examples/barseq_instrument.py

@@ -0,0 +1,250 @@
+"""Example BarSEQ instrument schema"""
+
+import argparse
+from datetime import date
+
+from aind_data_schema_models.modalities import Modality
+from aind_data_schema_models.organizations import Organization
+from aind_data_schema_models.units import SizeUnit
+
+from aind_data_schema.components.coordinates import CoordinateSystemLibrary
+from aind_data_schema.components.devices import (
+    Camera,
+    DAQDevice,
+    Device,
+    Filter,
+    Laser,
+    Microscope,
+    Objective,
+    Cooling,
+    DataInterface,
+    CameraChroma,
+    BinMode
+)
+from aind_data_schema.core.instrument import Instrument
+
+
+objectives = [
+    Objective(
+        name="20x Objective",
+        numerical_aperture=0.70,
+        magnification=20,
+        immersion="air",
+        manufacturer=Organization.NIKON,
+        model="CFI S Plan Fluor LWD 20XC",
+    ),
+]
+
+dichroics = [
+    Filter(
+        name="D1",
+        filter_type="Multiband",
+        manufacturer=Organization.SEMROCK,
+        model="FF421/491/567/659/776-Di01",
+        notes="DAPI/GFP/RFP/Cy5/Cy7 dichroic",
+        center_wavelength=[421, 491, 567, 659, 776],
+    ),
+    Filter(
+        name="D2",
+        filter_type="Multiband",
+        manufacturer=Organization.CHROMA,
+        model="ZT405/514/635rpc",
+        notes="DAPI/YFP/Rs Cy5 dichroic",
+        center_wavelength=[405, 514, 635],
+    ),
+    Filter(
+        name="D3",
+        filter_type="Multiband",
+        manufacturer=Organization.SEMROCK,
+        model="FF421/491/572-Di01-25x36",
+        notes="DAPI/GFP/TxRed dichroic",
+        center_wavelength=[421, 491, 572],
+    ),
+]
+
+emission_filters = [
+    Filter(
+        name="E1",
+        filter_type="Multiband",
+        manufacturer=Organization.SEMROCK,
+        model="FF01-441/511/593/684/817",
+        notes="DAPI/GFP/Red/Cy5/Cy7 - used with D1 and 405nm laser",
+        center_wavelength=[441, 511, 593, 684, 817],
+    ),
+    Filter(
+        name="E2",
+        filter_type="Band pass",
+        manufacturer=Organization.SEMROCK,
+        model="FF01-565/24",
+        notes="YFP - used with D2 and 520nm laser; bandwidth 24nm",
+        center_wavelength=565,
+    ),
+    Filter(
+        name="E3",
+        filter_type="Band pass",
+        manufacturer=Organization.SEMROCK,
+        model="FF01-585/11",
+        notes="RFP - used with D1 and 546nm laser; bandwidth 11nm",
+        center_wavelength=585,
+    ),
+    Filter(
+        name="E4",
+        filter_type="Band pass",
+        manufacturer=Organization.SEMROCK,
+        model="FF01-676/29",
+        notes="FarRed - used with D1 and 638nm laser; bandwidth 29nm",
+        center_wavelength=676,
+    ),
+    Filter(
+        name="E5",
+        filter_type="Band pass",
+        manufacturer=Organization.SEMROCK,
+        model="FF01-775/140",
+        notes="RS Cy5 - used with D2 and 638nm laser; bandwidth 140nm",
+        center_wavelength=775,
+    ),
+    Filter(
+        name="E6",
+        filter_type="Multiband",
+        manufacturer=Organization.SEMROCK,
+        model="FF01-391/477/549/639/741-25",
+        notes="YFP/Rs Cy5",
+        center_wavelength=[391, 477, 549, 639, 741],
+    ),
+    Filter(
+        name="E7",
+        filter_type="Multiband",
+        manufacturer=Organization.CHROMA,
+        model="69401m",
+        notes="DAPI/GFP/TxRed",
+        center_wavelength=[440, 520, 600],
+    ),
+    Filter(
+        name="E8",
+        filter_type="Multiband",
+        manufacturer=Organization.CHROMA,
+        model="ZET532/640m",
+        notes="Alexa532/Cy5(wide)",
+        center_wavelength=[532, 640],
+    ),
+]
+
+light_sources = [
+    Laser(
+        name="Lumencor Celesta 365nm",
+        manufacturer=Organization.LUMENCOR,
+        model="Celesta",
+        wavelength=365,
+    ),
+    Laser(
+        name="Lumencor Celesta 440nm",
+        manufacturer=Organization.LUMENCOR,
+        model="Celesta",
+        wavelength=440,
+    ),
+    Laser(
+        name="Lumencor Celesta 488nm",
+        manufacturer=Organization.LUMENCOR,
+        model="Celesta",
+        wavelength=488,
+    ),
+    Laser(
+        name="Lumencor Celesta 514nm",
+        manufacturer=Organization.LUMENCOR,
+        model="Celesta",
+        wavelength=514,
+    ),
+    Laser(
+        name="Lumencor Celesta 561nm",
+        manufacturer=Organization.LUMENCOR,
+        model="Celesta",
+        wavelength=561,
+    ),
+    Laser(
+        name="Lumencor Celesta 640nm",
+        manufacturer=Organization.LUMENCOR,
+        model="Celesta",
+        wavelength=640,
+    ),
+    Laser(
+        name="Lumencor Celesta 730nm",
+        manufacturer=Organization.LUMENCOR,
+        model="Celesta",
+        wavelength=730,
+    ),
+]
+
+camera = Camera(
+    name="Camera-1",
+    manufacturer=Organization.TELEDYNE_VISION_SOLUTIONS,
+    model="01-KINETIX-M-C",
+    data_interface=DataInterface.USB,
+    cooling=Cooling.AIR,
+    sensor_width=3200,
+    sensor_height=3200,
+    size_unit=SizeUnit.PX,
+    chroma=CameraChroma.BW,
+    immersion="air",
+    bin_mode=BinMode.NO_BINNING,
+    bit_depth=16,
+    sensor_format="20.8 x 20.8",
+    sensor_format_unit="mm",
+    frame_rate=500,
+    frame_rate_unit="hertz",
+)
+
+microscope = Microscope(
+    name="Ti2-E__0",
+    manufacturer=Organization.NIKON,
+    model="Ti2-E",
+)
+
+spinning_disk = Device(
+    name="XLIGHT Spinning Disk",
+    manufacturer=Organization.CRESTOPTICS,
+    model="X-Light V3",
+    notes="Nipkow spinning disk confocal module",
+)
+
+daq = DAQDevice(
+    name="DigitalIO",
+    manufacturer=Organization.NATIONAL_INSTRUMENTS,
+    model="NI-DAQ Dev1",
+    data_interface="USB",
+)
+
+instrument = Instrument(
+    location="243",
+    instrument_id="Dogwood",
+    modification_date=date(2024, 7, 9),
+    coordinate_system=CoordinateSystemLibrary.IMAGE_XYZ,
+    modalities=[Modality.BARSEQ],
+    notes=(
+        "BarSEQ imaging system with Nikon Ti2-E inverted microscope, X-Light V3 spinning disk confocal, "
+        "and Lumencor Celesta light engine. Used for multi-channel fluorescence imaging of genetically "
+        "modified tissue samples. Channel configurations: geneseq01/bcseq01 cycles use G/T/A/C/DAPI channels, "
+        "other geneseq/bcseq cycles use GTAC channels, hyb cycles use GFP/G/TxRed/Cy5/DAPI/DIC channels. "
+        "Camera pixel size: 0.33um. Stitch overlap: 23%. Hyb registration radius: 100um. "
+        "Configuration date corresponds to chprofile20x_dogwood_20240709.mat and chshift20x_dogwood_20240709.mat"
+    ),
+    temperature_control=False,
+    components=[
+        microscope,
+        *objectives,
+        *dichroics,
+        *emission_filters,
+        *light_sources,
+        camera,
+        spinning_disk,
+        daq,
+    ],
+)
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--output-dir", default=None, help="Output directory for generated JSON file")
+    args = parser.parse_args()
+
+    serialized = instrument.model_dump_json()
+    deserialized = Instrument.model_validate_json(serialized)
+    deserialized.write_standard_file(prefix="barseq", output_directory=args.output_dir)