An enhancement to core NWB schema types related to microscopy data.
Planned for an eventual NWBEP with the TAB.
git clone https://github.com/catalystneuro/ndx-microscopy
pip install ndx-microscopy
# TODOIn this PR I added neurodatatypes from ndx-ophys-devices:
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
classDiagram
direction TB
class DeviceModel {
<<Device>>
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attributes
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model : text, optional
}
class ExcitationLightPath {
<<LabMetaData>>
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attributes
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excitation_wavelength_in_nm : numeric
description : text
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links
--------------------------------------
excitation_source : ExcitationSource, optional
excitation_filter : OpticalFilter, optional
}
class EmissionLightPath {
<<LabMetaData>>
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attributes
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emission_wavelength_in_nm : numeric
description : text
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groups
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indicator : Indicator
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links
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photodetector : Photodetector, optional
emission_filter : OpticalFilter, optional
}
class ExcitationSource {
<<DeviceModel>>
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attributes
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illumination_type : text
excitation_wavelength_in_nm : float
power_in_W : float, optional
intensity_in_W_per_m2 : float, optional
exposure_time_in_s : float, optional
}
class PulsedExcitationSource {
<<ExcitationSource>>
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attributes
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peak_power_in_W : float, optional
peak_pulse_energy_in_J : float, optional
pulse_rate_in_Hz : float, optional
}
class OpticalFilter {
<<DeviceModel>>
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attributes
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filter_type : text
}
class BandOpticalFilter {
<<OpticalFilter>>
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attributes
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center_wavelength_in_nm : float
bandwidth_in_nm : float
}
class EdgeOpticalFilter {
<<OpticalFilter>>
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attributes
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cut_wavelength_in_nm : float
slope_in_percent_cut_wavelength : float, optional
slope_starting_transmission_in_percent : float, optional
slope_ending_transmission_in_percent : float, optional
}
class Photodetector {
<<DeviceModel>>
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attributes
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detector_type : text
detected_wavelength_in_nm : float
gain : float, optional
gain_unit : text, optional
}
class Indicator {
<<NWBContainer>>
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attributes
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label : text
description : text, optional
manufacturer : text, optional
injection_brain_region : text, optional
injection_coordinates_in_mm : float[3], optional
}
DeviceModel <|-- ExcitationSource : extends
DeviceModel <|-- OpticalFilter : extends
DeviceModel <|-- Photodetector : extends
ExcitationSource <|-- PulsedExcitationSource : extends
OpticalFilter <|-- BandOpticalFilter : extends
OpticalFilter <|-- EdgeOpticalFilter : extends
ExcitationLightPath ..> ExcitationSource : links
ExcitationLightPath ..> OpticalFilter : links
EmissionLightPath ..> Photodetector : links
EmissionLightPath ..> OpticalFilter : links
EmissionLightPath *-- Indicator : contains
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
classDiagram
direction BT
class MicroscopySeries {
<<TimeSeries>>
--------------------------------------
links
--------------------------------------
microscope : Microscope
excitation_light_path : ExcitationLightPath
emission_light_path : EmissionLightPath
}
class PlanarMicroscopySeries {
<<MicroscopySeries>>
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datasets
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data : numeric, frame x height x width
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links
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imaging_space : PlanarImagingSpace
}
class VariableDepthMicroscopySeries {
<<PlanarMicroscopySeries>>
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datasets
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depth_per_frame_in_um : numeric, length of frames
}
class VolumetricMicroscopySeries {
<<MicroscopySeries>>
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datasets
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data : numeric, frame x height x width x depth
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links
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imaging_space : VolumetricImagingSpace
}
class MultiChannelMicroscopyVolume {
<<NWBDataInterface>>
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attributes
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description : text, optional
unit : text
conversion : float32, optional, default=1.0
offset : float32, optional, default=0.0
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datasets
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data : numeric, height x width x depth x emission_light_paths
excitation_light_paths : ExcitationLightPath[]
emission_light_paths : EmissionLightPath[]
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links
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imaging_space : VolumetricImagingSpace
microscope : Microscope
}
class ImagingSpace {
<<LabMetaData>>
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datasets
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description : text
origin_coordinates : float64[3], optional
--> unit : text, default="micrometers"
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attributes
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location : text, optional
}
class PlanarImagingSpace {
<<ImagingSpace>>
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datasets
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grid_spacing_in_um : float64[2], optional
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attributes
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reference_frame : text, optional
}
class VolumetricImagingSpace {
<<ImagingSpace>>
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datasets
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grid_spacing_in_um : float64[3], optional
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attributes
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reference_frame : text, optional
}
class ExcitationLightPath {
<<LabMetaData>>
--------------------------------------
attributes
--------------------------------------
excitation_wavelength_in_nm : numeric
description : text
--------------------------------------
links
--------------------------------------
excitation_source : ExcitationSource, optional
excitation_filter : OpticalFilter, optional
}
class EmissionLightPath {
<<LabMetaData>>
--------------------------------------
attributes
--------------------------------------
emission_wavelength_in_nm : numeric
description : text
--------------------------------------
groups
--------------------------------------
indicator : Indicator
--------------------------------------
links
--------------------------------------
photodetector : Photodetector, optional
emission_filter : OpticalFilter, optional
}
class Microscope {
<<Device>>
--------------------------------------
attributes
--------------------------------------
model : text, optional
}
PlanarMicroscopySeries *-- MicroscopySeries : extends
PlanarMicroscopySeries -- PlanarImagingSpace : links
VariableDepthMicroscopySeries *-- PlanarMicroscopySeries : extends
VolumetricMicroscopySeries *-- MicroscopySeries : extends
VolumetricMicroscopySeries -- VolumetricImagingSpace : links
MultiChannelMicroscopyVolume -- VolumetricImagingSpace : links
PlanarImagingSpace *-- ImagingSpace : extends
VolumetricImagingSpace *-- ImagingSpace : extends
MicroscopySeries ..> Microscope : links
MicroscopySeries ..> ExcitationLightPath : links
MicroscopySeries ..> EmissionLightPath : links
This extension was created using ndx-template.