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chore: build ISI instrument example (#1833)
* examples: draft instrument * chore: bump version, clean up notes, add organizations * update docs * chore: some more cleanup * refactor: rename devices * update docs --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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‎docs/source/aind_data_schema_models/process_names.md‎

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| `IMAGE_TILE_ALIGNMENT` | `Image tile alignment` |
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| `IMAGE_TILE_FUSING` | `Image tile fusing` |
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| `IMAGE_TILE_PROJECTION` | `Image tile projection` |
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| `MANUAL_CURATION` | `Manual curation` |
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| `MODEL_EVALUATION` | `Model evaluation` |
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| `MODEL_TRAINING` | `Model training` |
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| `NEURON_SKELETON_PROCESSING` | `Neuron skeleton processing` |

‎examples/isi_instrument.py‎

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

‎pyproject.toml‎

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dynamic = ["version"]
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dependencies = [
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'aind-data-schema-models>=5.4.1,<6',
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'aind-data-schema-models>=5.7.1,<6',
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'pydantic>=2.7, <2.12',
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'pydantic-extra-types',
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'tzdata',

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