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Merge pull request #544 from AllenNeuralDynamics/feat-344-slap
Feat 344 slap
2 parents 9967a02 + a46dc1c commit d17b928

15 files changed

+129
-27
lines changed

‎examples/aibs_smartspim_instrument.json‎

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{
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"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py",
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"schema_version": "0.9.1",
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"schema_version": "0.9.2",
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"instrument_id": "SmartSPIM2-2",
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"modification_date": "2023-10-04",
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"instrument_type": "SmartSPIM",
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"notes": "Thorlabs TL4X-SAP with LifeCanvas dipping cap and correction optics.",
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"numerical_aperture": 0.2,
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"magnification": 3.6,
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"immersion": "multi"
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"immersion": "multi",
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"objective_type": null
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}
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],
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"detectors": [

‎examples/aind_smartspim_instrument.json‎

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{
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"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py",
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"schema_version": "0.9.1",
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"schema_version": "0.9.2",
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"instrument_id": "SmartSPIM1-3",
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"modification_date": "2023-10-04",
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"instrument_type": "SmartSPIM",
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"notes": "",
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"numerical_aperture": 0.1,
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"magnification": 1.6,
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"immersion": "multi"
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"immersion": "multi",
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"objective_type": null
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},
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{
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"device_type": "Objective",
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"notes": "Thorlabs TL4X-SAP with LifeCanvas dipping cap and correction optics",
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"numerical_aperture": 0.2,
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"magnification": 3.6,
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"immersion": "multi"
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"immersion": "multi",
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"objective_type": null
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},
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{
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"device_type": "Objective",
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"notes": "",
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"numerical_aperture": 0.8,
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"magnification": 16.0,
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"immersion": "water"
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"immersion": "water",
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"objective_type": null
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},
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{
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"device_type": "Objective",
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"notes": "",
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"numerical_aperture": 1.1,
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"magnification": 25.0,
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"immersion": "water"
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"immersion": "water",
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"objective_type": null
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}
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],
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"detectors": [

‎examples/bergamo_ophys_session.json‎

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{
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"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",
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"schema_version": "0.0.2",
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"schema_version": "0.0.3",
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"experimenter_full_name": [
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"John Doe"
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],
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"rig_id": "ophys_rig",
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"calibrations": null,
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"maintenance": null,
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"subject_id": 652567,
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"subject_id": "652567",
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"animal_weight_prior": null,
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"animal_weight_post": null,
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"weight_unit": "gram",
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"coupled_fov_index": null
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}
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],
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"slap_fovs": null,
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"stack_parameters": null,
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"stimulus_device_names": null,
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"notes": null

‎examples/ephys_rig.json‎

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{
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"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/rig.py",
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"schema_version": "0.1.2",
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"schema_version": "0.1.3",
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"rig_id": "323_EPHYS1",
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"modification_date": "2023-10-03",
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"modalities": [
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"objectives": null,
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"filters": null,
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"lenses": null,
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"digital_micromirror_devices": null,
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"polygonal_scanners": null,
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"pockels_cells": null,
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"additional_devices": null,
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"calibrations": [
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{

‎examples/ephys_session.json‎

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{
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"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",
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"schema_version": "0.0.2",
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"schema_version": "0.0.3",
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"experimenter_full_name": [
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"Jane Doe"
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],
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"rig_id": "323_EPHYS1",
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"calibrations": null,
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"maintenance": null,
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"subject_id": 100001,
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"subject_id": "100001",
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"animal_weight_prior": 21.2,
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"animal_weight_post": 21.3,
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"weight_unit": "gram",
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"detectors": null,
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"fiber_photometry_assemblies": null,
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"ophys_fovs": null,
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"slap_fovs": null,
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"stack_parameters": null,
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"stimulus_device_names": null,
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"notes": null

‎examples/exaspim_instrument.json‎

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{
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"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py",
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"schema_version": "0.9.1",
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"schema_version": "0.9.2",
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"instrument_id": "exaSPIM1-1",
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"modification_date": "2023-10-04",
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"instrument_type": "exaSPIM",
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"notes": "manufacturer collaboration between Schneider-Kreuznach and Vieworks",
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"numerical_aperture": 0.305,
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"magnification": 5,
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"immersion": "air"
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"immersion": "air",
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"objective_type": null
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}
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],
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"detectors": [

‎examples/fip_ophys_rig.json‎

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{
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"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/rig.py",
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"schema_version": "0.1.2",
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"schema_version": "0.1.3",
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"rig_id": "428_FIP1_2",
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"modification_date": "2023-10-03",
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"modalities": [
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"notes": null,
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"numerical_aperture": 0.45,
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"magnification": 10,
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"immersion": "air"
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"immersion": "air",
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"objective_type": null
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}
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],
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"filters": [
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"max_aperture": null
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}
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],
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"digital_micromirror_devices": null,
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"polygonal_scanners": null,
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"pockels_cells": null,
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"additional_devices": null,
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"calibrations": [
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{

‎examples/ophys_session.json‎

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{
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"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",
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"schema_version": "0.0.2",
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"schema_version": "0.0.3",
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"experimenter_full_name": [
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"John Doe"
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],
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"rig_id": "ophys_rig",
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"calibrations": null,
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"maintenance": null,
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"subject_id": 652567,
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"subject_id": "652567",
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"animal_weight_prior": null,
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"animal_weight_post": null,
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"weight_unit": "gram",
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}
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],
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"ophys_fovs": null,
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"slap_fovs": null,
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"stack_parameters": null,
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"stimulus_device_names": null,
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"notes": "Internal trigger. GRAB-DA2m shows signal. Unclear about GRAB-rAC"

‎src/aind_data_schema/device.py‎

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from aind_data_schema.coordinates import RelativePosition
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from aind_data_schema.manufacturers import Manufacturer
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from aind_data_schema.procedures import Reagent
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from aind_data_schema.utils.units import FrequencyUnit, PowerUnit, SizeUnit, TemperatureUnit
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from aind_data_schema.utils.units import FrequencyUnit, PowerUnit, SizeUnit, SpeedUnit, TemperatureUnit, UnitlessUnit
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class DeviceDriver(Enum):
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OTHER = "other"
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class ObjectiveType(Enum):
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"""Objective type for Slap2"""
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REMOTE = "Remote"
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PRIMARY = "Primary"
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class Objective(Device):
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"""Description of an objective device"""
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device_type: Literal["Objective"] = Field("Objective", const=True, readOnly=True)
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numerical_aperture: Decimal = Field(..., title="Numerical aperture (in air)")
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magnification: Decimal = Field(..., title="Magnification")
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immersion: Immersion = Field(..., title="Immersion")
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objective_type: Optional[ObjectiveType] = Field(None, title="Objective type")
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class CameraTarget(Enum):
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photobleaching_date: Optional[date] = Field(None, title="Photobleaching date")
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class DigitalMicromirrorDevice(Device):
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"""Description of a Digital Micromirror Device (DMD)"""
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device_type: Literal["Digital Micromirror Device"] = Field("Digital Micromirror Device", const=True, readOnly=True)
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max_dmd_patterns: int = Field(..., title="Max DMD patterns")
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double_bounce_design: bool = Field(..., title="Double bounce design")
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invert_pixel_values: bool = Field(..., title="Invert pixel values")
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motion_padding_x: int = Field(..., title="Motion padding X (pixels)")
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motion_padding_y: int = Field(..., title="Motion padding Y (pixels)")
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padding_unit: SizeUnit = Field(SizeUnit.PX, title="Padding unit")
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pixel_size: Decimal = Field(..., title="DMD Pixel size")
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pixel_size_unit: SizeUnit = Field(SizeUnit.UM, title="Pixel size unit")
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start_phase: Decimal = Field(..., title="DMD Start phase (fraction of cycle)")
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dmd_flip: bool = Field(..., title="DMD Flip")
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dmd_curtain: List[Decimal] = Field(..., title="DMD Curtain")
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dmd_curtain_unit: SizeUnit = Field(SizeUnit.PX, title="dmd_curtain_unit")
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line_shear: List[int] = Field(..., title="Line shear (pixels)")
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line_shear_units: SizeUnit = Field(SizeUnit.PX, title="Line shear units")
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class PolygonalScanner(Device):
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"""Description of a Polygonal scanner"""
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device_type: Literal["Polygonal Scanner"] = Field("Polygonal Scanner", const=True, readOnly=True)
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speed: int = Field(..., title="Speed (rpm)")
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speed_unit: SpeedUnit = Field(SpeedUnit.RPM, title="Speed unit")
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number_faces: int = Field(..., title="Number of faces")
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class PockelsCell(Device):
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"""Description of a Pockels Cell"""
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device_type: Literal["Pockels Cell"] = Field("Pockels Cell", const=True, readOnly=True)
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polygonal_scanner: str = Field(..., title="Polygonal scanner", description="Must match name of Polygonal scanner")
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on_time: Decimal = Field(..., title="On time (fraction of cycle)")
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off_time: Decimal = Field(..., title="Off time (fraction of cycle)")
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time_setting_unit: UnitlessUnit = Field(UnitlessUnit.FC, title="time setting unit")
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class MousePlatform(Device):
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"""Description of a mouse platform"""
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‎src/aind_data_schema/imaging/instrument.py‎

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class Instrument(AindCoreModel):
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"""Description of an instrument, which is a collection of devices"""
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schema_version: str = Field("0.9.1", description="schema version", title="Version", const=True)
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schema_version: str = Field("0.9.2", description="schema version", title="Version", const=True)
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instrument_id: Optional[str] = Field(
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None,
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description="Unique identifier for this instrument. Naming convention: <room>-<apparatus>-<version>",

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