chore: build ISI instrument example

docs/source/aind_data_schema_models/process_names.md

@@ -37,6 +37,7 @@ Process names
 | `IMAGE_TILE_ALIGNMENT` | `Image tile alignment` |
 | `IMAGE_TILE_FUSING` | `Image tile fusing` |
 | `IMAGE_TILE_PROJECTION` | `Image tile projection` |
+| `MANUAL_CURATION` | `Manual curation` |
 | `MODEL_EVALUATION` | `Model evaluation` |
 | `MODEL_TRAINING` | `Model training` |
 | `NEURON_SKELETON_PROCESSING` | `Neuron skeleton processing` |

examples/isi_instrument.py

@@ -0,0 +1,248 @@
+"""Generates an example JSON file for an ISI (Intrinsic Signal Imaging) instrument
+
+Based on the ISI Full Rig BOM (AIBS part 0113_000-00, Rev A).
+The rig consists of:
+  - ISI Table Assembly (0113_100-00)
+  - ISI System Structure (0113_200-00)
+  - Camera, Stage, and Mount Assembly (0113_300-00)
+  - Headframe Clamp Assembly (0113_400-00)
+  - ISI Eye Tracking Assembly (0123_500-00)
+  - Camera/Lens Assembly (0113_550-00) with tandem Nikon lenses and Andor Zyla sCMOS
+  - LED Light Ring Assembly (0113_530-00)
+"""
+
+import argparse
+from datetime import date
+
+from aind_data_schema_models.coordinates import AnatomicalRelative
+from aind_data_schema_models.devices import (
+    CameraChroma,
+    CameraTarget,
+    DataInterface,
+    DetectorType,
+    FilterType,
+)
+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,
+    CameraAssembly,
+    Computer,
+    DAQDevice,
+    Device,
+    Filter,
+    Lens,
+    LightEmittingDiode,
+    Monitor,
+    MotorizedStage,
+)
+from aind_data_schema.core.instrument import Instrument
+
+acquisition_computer = Computer(
+    name="Acquisition Computer",
+)
+
+stim_computer = Computer(
+    name="Stim Computer",
+)
+
+ni_daq = DAQDevice(
+    name="DAQ",
+    manufacturer=Organization.NATIONAL_INSTRUMENTS,
+    model="USB-6008",
+    data_interface=DataInterface.USB,
+)
+
+newport_linear_stage = MotorizedStage(
+    name="Linear Stage",
+    manufacturer=Organization.MKS_NEWPORT,
+    model="M-ILS100PP",
+    travel=100,
+    travel_unit=SizeUnit.MM,
+    notes="Controlled by Newport SMC100PP.",
+)
+
+newport_motor_controller = Device(
+    name="Motor Controller",
+    manufacturer=Organization.MKS_NEWPORT,
+    model="SMC100PP",
+)
+
+isi_camera = Camera(
+    name="ISI Camera",
+    manufacturer=Organization.OXFORD_INSTRUMENTS,
+    model="Zyla 5.5 sCMOS",
+    detector_type=DetectorType.CAMERA,
+    data_interface=DataInterface.USB,
+    chroma=CameraChroma.BW,
+)
+
+isi_lens_35mm = Lens(
+    name="Front Lens",
+    manufacturer=Organization.NIKON,
+    model="NIKKOR 35mm f/1.4",
+    notes="Front lens of tandem-lens assembly.",
+)
+
+isi_lens_105mm = Lens(
+    name="Rear Lens",
+    manufacturer=Organization.NIKON,
+    model="Micro-NIKKOR 105mm f/2.8",
+    notes="Rear lens of tandem-lens assembly, facing the camera.",
+)
+
+isi_bandpass_filter = Filter(
+    name="Bandpass Filter",
+    manufacturer=Organization.SEMROCK,
+    model="FF01-630/92-50",
+    filter_type=FilterType.BANDPASS,
+    center_wavelength=630,
+    wavelength_unit=SizeUnit.NM,
+)
+
+isi_camera_assembly = CameraAssembly(
+    name="ISI Brain Camera Assembly",
+    target=CameraTarget.BRAIN,
+    relative_position=[AnatomicalRelative.SUPERIOR],
+    camera=isi_camera,
+    lens=isi_lens_35mm,
+    filter=isi_bandpass_filter,
+)
+
+eye_tracking_camera = Camera(
+    name="Eye Tracking Camera",
+    manufacturer=Organization.ALLIED,
+    model="MAKO G-125C",
+    detector_type=DetectorType.CAMERA,
+    data_interface=DataInterface.ETH,
+    chroma=CameraChroma.BW,
+)
+
+eye_tracking_lens = Lens(
+    name="Eye Tracking Lens",
+    manufacturer=Organization.INFINITY_PHOTO_OPTICAL,
+    model="Proximity Series 130mm W.D./0.73x",
+)
+
+eye_tracking_camera_assembly = CameraAssembly(
+    name="Eye Tracking Camera Assembly",
+    target=CameraTarget.EYE,
+    relative_position=[AnatomicalRelative.ANTERIOR],
+    camera=eye_tracking_camera,
+    lens=eye_tracking_lens,
+)
+
+eye_tracking_dichroic = Filter(
+    name="Dichroic Filter",
+    manufacturer=Organization.SEMROCK,
+    model="FF750-SDi02-25x36",
+    filter_type=FilterType.DICHROIC,
+    cut_off_wavelength=750,
+    wavelength_unit=SizeUnit.NM,
+    notes="Separates 850 nm IR illumination for eye tracking.",
+)
+
+eye_tracking_ir_led = LightEmittingDiode(
+    name="Eye Tracking IR LED",
+    manufacturer=Organization.AMS_OSRAM,
+    model="LZ4-40R608-0000",
+    wavelength=850,
+    wavelength_unit=SizeUnit.NM,
+)
+
+eye_tracking_collimating_lens = Lens(
+    name="Collimating Lens",
+    manufacturer=Organization.THORLABS,
+    model="LB1092-B-ML",
+)
+
+led_ring_green = LightEmittingDiode(
+    name="LED Ring Green",
+    manufacturer=Organization.OTHER,
+    model="C503B-GCN-CY0C0791",
+    wavelength=527,
+    wavelength_unit=SizeUnit.NM,
+    notes="19 units in LED light ring assembly (0113_530-00).",
+)
+
+led_ring_red = LightEmittingDiode(
+    name="LED Ring Red",
+    manufacturer=Organization.OTHER,
+    model="HLMP-EG08-Y2000",
+    wavelength=635,
+    wavelength_unit=SizeUnit.NM,
+    notes="9 units in LED light ring assembly (0113_530-00).",
+)
+
+stimulus_monitor = Monitor(
+    name="Stimulus Monitor",
+    manufacturer=Organization.ASUS,
+    model="PA248Q",
+    refresh_rate=60,
+    width=1920,
+    height=1200,
+    size_unit=SizeUnit.PX,
+    viewing_distance=15,
+    viewing_distance_unit=SizeUnit.CM,
+    relative_position=[AnatomicalRelative.ANTERIOR],
+)
+
+temperature_controller = Device(
+    name="Temperature Controller",
+    manufacturer=Organization.WPI,
+    model="ATC2000",
+)
+
+somnosuite = Device(
+    name="SomnoSuite",
+    manufacturer=Organization.KENT_SCIENTIFIC_CORPORATION,
+    model="SOMNO",
+    notes="Used with accessory facemasks (SOMNO-0801) and induction chamber (SOMNO-0705).",
+)
+
+physiosuite = Device(
+    name="PhysioSuite",
+    manufacturer=Organization.KENT_SCIENTIFIC_CORPORATION,
+    model="PS-MSTAT-RT",
+)
+
+inst = Instrument(
+    location="",
+    instrument_id="ISIV.1",
+    modification_date=date(2026, 5, 15),
+    modalities=[Modality.ISI],
+    coordinate_system=CoordinateSystemLibrary.BREGMA_ARI,
+    temperature_control=True,
+    notes="",
+    components=[
+        acquisition_computer,
+        stim_computer,
+        ni_daq,
+        newport_linear_stage,
+        newport_motor_controller,
+        isi_camera_assembly,
+        isi_lens_105mm,
+        eye_tracking_camera_assembly,
+        eye_tracking_dichroic,
+        eye_tracking_ir_led,
+        eye_tracking_collimating_lens,
+        led_ring_green,
+        led_ring_red,
+        stimulus_monitor,
+        temperature_controller,
+        somnosuite,
+        physiosuite,
+    ],
+)
+
+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 = inst.model_dump_json()
+    deserialized = Instrument.model_validate_json(serialized)
+    deserialized.write_standard_file(prefix="isi", output_directory=args.output_dir)

pyproject.toml

@@ -14,7 +14,7 @@ readme = "README.md"
 dynamic = ["version"]
 
 dependencies = [
-    'aind-data-schema-models>=5.4.1,<6',
+    'aind-data-schema-models>=5.7.1,<6',
     'pydantic>=2.7, <2.12',
     'pydantic-extra-types',
     'tzdata',