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Merge branch 'main' into feat-500-add-AnalysisDescription
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‎docs/source/_static/diagrams/Instrument.png‎

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‎docs/source/_static/diagrams/OphysRig.png‎

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‎docs/source/_static/diagrams/Rig.png‎

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‎examples/aibs_smartspim_instrument.json‎

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@@ -1,6 +1,6 @@
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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",
3-
"schema_version": "0.8.2",
3+
"schema_version": "0.9.1",
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"instrument_id": "SmartSPIM2-2",
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"modification_date": "2023-10-04",
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"instrument_type": "SmartSPIM",
@@ -68,14 +68,28 @@
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},
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"model": "C14440-20UP",
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"notes": null,
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"type": "Camera",
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"detector_type": "Camera",
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"data_interface": "USB",
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"cooling": "air"
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"cooling": "air",
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"immersion": null,
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"chroma": null,
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"sensor_width": null,
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"sensor_height": null,
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"size_unit": "pixel",
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"bit_depth": null,
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"bin_mode": "none",
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"bin_width": null,
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"bin_height": null,
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"bin_unit": "pixel",
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"gain": null,
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"crop_width": null,
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"crop_height": null,
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"crop_unit": "pixel"
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}
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],
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"light_sources": [
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{
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"device_type": "Lightsource",
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"device_type": "Laser",
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"name": "Ex_488",
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"serial_number": "VL01222A11",
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"manufacturer": {
@@ -86,15 +100,17 @@
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},
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"model": "Stradus",
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"notes": "All lasers controlled via Vortran VersaLase System",
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"type": "laser",
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"coupling": "Single-mode fiber",
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"wavelength": 488,
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"wavelength_unit": "nanometer",
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"max_power": 150,
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"power_unit": "milliwatt"
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"maximum_power": 150,
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"power_unit": "milliwatt",
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"coupling": "Single-mode fiber",
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"coupling_efficiency": null,
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"coupling_efficiency_unit": "percent",
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"item_number": null
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},
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{
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"device_type": "Lightsource",
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"device_type": "Laser",
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"name": "Ex_561",
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"serial_number": "417927",
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"manufacturer": {
@@ -108,15 +124,17 @@
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},
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"model": "Obis",
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"notes": "All lasers controlled via Vortran VersaLase System",
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"type": "laser",
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"coupling": "Single-mode fiber",
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"wavelength": 561,
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"wavelength_unit": "nanometer",
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"max_power": 150,
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"power_unit": "milliwatt"
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"maximum_power": 150,
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"power_unit": "milliwatt",
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"coupling": "Single-mode fiber",
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"coupling_efficiency": null,
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"coupling_efficiency_unit": "percent",
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"item_number": null
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},
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{
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"device_type": "Lightsource",
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"device_type": "Laser",
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"name": "Ex_647",
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"serial_number": "VL01222A10",
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"manufacturer": {
@@ -127,14 +145,17 @@
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},
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"model": "Stradus",
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"notes": "All lasers controlled via Vortran VersaLase System",
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"type": "laser",
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"coupling": "Single-mode fiber",
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"wavelength": 647,
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"wavelength_unit": "nanometer",
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"max_power": 160,
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"power_unit": "milliwatt"
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"maximum_power": 160,
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"power_unit": "milliwatt",
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"coupling": "Single-mode fiber",
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"coupling_efficiency": null,
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"coupling_efficiency_unit": "percent",
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"item_number": null
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}
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],
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"lenses": null,
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"fluorescence_filters": [
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{
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"device_type": "Filter",

‎examples/aibs_smartspim_instrument.py‎

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Original file line numberDiff line numberDiff line change
@@ -1,19 +1,9 @@
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""" example SmartSPIM instrument """
22
import datetime
33

4-
from aind_data_schema.device import Manufacturer
5-
from aind_data_schema.imaging.instrument import (
6-
AdditionalImagingDevice,
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Com,
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Detector,
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Filter,
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Instrument,
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Lightsource,
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MotorizedStage,
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Objective,
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OpticalTable,
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ScanningStage,
16-
)
4+
from aind_data_schema.device import Detector, Filter, Laser, MotorizedStage, Objective
5+
from aind_data_schema.imaging.instrument import AdditionalImagingDevice, Com, Instrument, OpticalTable, ScanningStage
6+
from aind_data_schema.manufacturers import Manufacturer
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inst = Instrument(
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instrument_id="SmartSPIM2-2",
@@ -33,7 +23,7 @@
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],
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detectors=[
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Detector(
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type="Camera",
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detector_type="Camera",
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data_interface="USB",
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cooling="air",
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manufacturer=Manufacturer.HAMAMATSU,
@@ -42,34 +32,34 @@
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),
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],
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light_sources=[
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Lightsource(
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Laser(
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name="Ex_488",
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type="laser",
37+
device_type="Laser",
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coupling="Single-mode fiber",
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wavelength=488,
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max_power=150,
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maximum_power=150,
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serial_number="VL01222A11",
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manufacturer=Manufacturer.VORTRAN,
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model="Stradus",
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notes="All lasers controlled via Vortran VersaLase System",
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),
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Lightsource(
46+
Laser(
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name="Ex_561",
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type="laser",
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device_type="Laser",
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coupling="Single-mode fiber",
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wavelength=561,
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max_power=150,
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maximum_power=150,
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serial_number="417927",
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manufacturer=Manufacturer.COHERENT_SCIENTIFIC,
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model="Obis",
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notes="All lasers controlled via Vortran VersaLase System",
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),
67-
Lightsource(
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Laser(
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name="Ex_647",
69-
type="laser",
59+
device_type="Laser",
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coupling="Single-mode fiber",
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wavelength=647,
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max_power=160,
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maximum_power=160,
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serial_number="VL01222A10",
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manufacturer=Manufacturer.VORTRAN,
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model="Stradus",

‎examples/aind_smartspim_instrument.json‎

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Original file line numberDiff line numberDiff line change
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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",
3-
"schema_version": "0.8.2",
3+
"schema_version": "0.9.1",
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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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},
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"model": "C14440-20UP",
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"notes": null,
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"type": "Camera",
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"detector_type": "Camera",
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"data_interface": "USB",
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"cooling": "water"
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"cooling": "water",
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"immersion": null,
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"chroma": null,
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"sensor_width": null,
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"sensor_height": null,
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"size_unit": "pixel",
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"bit_depth": null,
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"bin_mode": "none",
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"bin_width": null,
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"bin_height": null,
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"bin_unit": "pixel",
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"gain": null,
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"crop_width": null,
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"crop_height": null,
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"crop_unit": "pixel"
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}
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],
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"light_sources": [
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{
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"device_type": "Lightsource",
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"device_type": "Laser",
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"name": "Ex_445",
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"serial_number": "VL08223M03",
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"manufacturer": {
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},
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"model": "Stradus",
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"notes": "All lasers controlled via Vortran VersaLase System",
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"type": "laser",
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"coupling": "Single-mode fiber",
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"wavelength": 445,
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"wavelength_unit": "nanometer",
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"max_power": 150,
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"power_unit": "milliwatt"
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"maximum_power": 150,
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"power_unit": "milliwatt",
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"coupling": "Single-mode fiber",
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"coupling_efficiency": null,
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"coupling_efficiency_unit": "percent",
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"item_number": null
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},
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{
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"device_type": "Lightsource",
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"device_type": "Laser",
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"name": "Ex_488",
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"serial_number": "VL08223M03",
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"manufacturer": {
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},
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"model": "Stradus",
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"notes": "All lasers controlled via Vortran VersaLase System",
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"type": "laser",
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"coupling": "Single-mode fiber",
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"wavelength": 488,
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"wavelength_unit": "nanometer",
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"max_power": 150,
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"power_unit": "milliwatt"
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"maximum_power": 150,
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"power_unit": "milliwatt",
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"coupling": "Single-mode fiber",
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"coupling_efficiency": null,
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"coupling_efficiency_unit": "percent",
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"item_number": null
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},
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{
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"device_type": "Lightsource",
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"device_type": "Laser",
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"name": "Ex_561",
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"serial_number": "VL08223M03",
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"manufacturer": {
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},
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"model": "Stradus",
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"notes": "All lasers controlled via Vortran VersaLase System",
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"type": "laser",
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"coupling": "Single-mode fiber",
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"wavelength": 561,
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"wavelength_unit": "nanometer",
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"max_power": 150,
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"power_unit": "milliwatt"
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"maximum_power": 150,
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"power_unit": "milliwatt",
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"coupling": "Single-mode fiber",
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"coupling_efficiency": null,
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"coupling_efficiency_unit": "percent",
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"item_number": null
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},
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{
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"device_type": "Lightsource",
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"device_type": "Laser",
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"name": "Ex_594",
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"serial_number": "VL08223M03",
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"manufacturer": {
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},
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"model": "Stradus",
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"notes": "All lasers controlled via Vortran VersaLase System",
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"type": "laser",
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"coupling": "Single-mode fiber",
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"wavelength": 594,
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"wavelength_unit": "nanometer",
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"max_power": 150,
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"power_unit": "milliwatt"
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"maximum_power": 150,
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"power_unit": "milliwatt",
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"coupling": "Single-mode fiber",
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"coupling_efficiency": null,
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"coupling_efficiency_unit": "percent",
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"item_number": null
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},
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{
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"device_type": "Lightsource",
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"device_type": "Laser",
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"name": "Ex_639",
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"serial_number": "VL08223M03",
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"manufacturer": {
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},
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"model": "Stradus",
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"notes": "All lasers controlled via Vortran VersaLase System",
225-
"type": "laser",
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"coupling": "Single-mode fiber",
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"wavelength": 639,
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"wavelength_unit": "nanometer",
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"max_power": 160,
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"power_unit": "milliwatt"
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"maximum_power": 160,
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"power_unit": "milliwatt",
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"coupling": "Single-mode fiber",
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"coupling_efficiency": null,
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"coupling_efficiency_unit": "percent",
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"item_number": null
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},
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{
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"device_type": "Lightsource",
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"device_type": "Laser",
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"name": "Ex_665",
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"serial_number": "VL08223M03",
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"manufacturer": {
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},
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"model": "Stradus",
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"notes": "All lasers controlled via Vortran VersaLase System",
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"type": "laser",
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"coupling": "Single-mode fiber",
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"wavelength": 665,
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"wavelength_unit": "nanometer",
248-
"max_power": 160,
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"power_unit": "milliwatt"
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"maximum_power": 160,
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"power_unit": "milliwatt",
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"coupling": "Single-mode fiber",
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"coupling_efficiency": null,
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"coupling_efficiency_unit": "percent",
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"item_number": null
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}
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],
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"lenses": null,
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"fluorescence_filters": [
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{
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"device_type": "Filter",

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