An NWB extension to demonstrate the TAB proposal for enhancements to optical physiology neurodata types.
Project description
ndx-microscopy Extension for NWB
A Neurodata Without Borders (NWB) extension for storing microscopy data and associated metadata in a standardized format. This extension integrates with ndx-ophys-devices to provide comprehensive optical component specifications.
Features
Comprehensive Neurodata Types
- Microscope and optical component metadata (integration with ndx-ophys-devices):
MicroscopeExcitationSource/PulsedExcitationSourceBandOpticalFilter/EdgeOpticalFilter/DichroicMirrorPhotodetectorIndicator
- Advanced light path configurations:
ExcitationLightPathEmissionLightPath
- Imaging space definitions:
PlanarImagingSpaceVolumetricImagingSpace
- Illumination pattern classes:
IlluminationPatternLineScanPlaneAcquisitionRandomAccessScan
- Support for 2D and 3D imaging:
PlanarMicroscopySeriesVolumetricMicroscopySeriesMultiPlaneMicroscopyContainer
- ROI/segmentation storage:
Segmentation2DSegmentation3DSegmentationContainerMicroscopyResponseSeriesMicroscopyResponseSeriesContainer
- Abstract Neurodata types:
ImagingSpace,MicroscopySeries,Segmentation
Entity Relationship Diagrams
Device and Light Path Components
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
classDiagram
direction TB
class DeviceModel {
<<Device>>
--------------------------------------
attributes
--------------------------------------
model : text, optional
}
class ExcitationLightPath {
<<LabMetaData>>
--------------------------------------
attributes
--------------------------------------
**description** : text
--------------------------------------
links
--------------------------------------
**excitation_source** : ExcitationSource
excitation_filter : OpticalFilter, optional
dichroic_mirror : DichroicMirror, optional
--------------------------------------
methods
--------------------------------------
get_excitation_wavelength()
}
class EmissionLightPath {
<<LabMetaData>>
--------------------------------------
attributes
--------------------------------------
**description** : text
--------------------------------------
groups
--------------------------------------
**indicator** : Indicator
--------------------------------------
links
--------------------------------------
**photodetector** : Photodetector
emission_filter : OpticalFilter, optional
dichroic_mirror : DichroicMirror, optional
--------------------------------------
methods
--------------------------------------
get_emission_wavelength()
get_indicator_label()
}
class ExcitationSource {
<<DeviceModel>>
--------------------------------------
attributes
--------------------------------------
**illumination_type** : text
**excitation_wavelength_in_nm** : float
**excitation_mode** : text
power_in_W : float, optional
intensity_in_W_per_m2 : float, optional
exposure_time_in_s : float, optional
}
class PulsedExcitationSource {
<<ExcitationSource>>
--------------------------------------
attributes
--------------------------------------
peak_power_in_W : float, optional
peak_pulse_energy_in_J : float, optional
pulse_rate_in_Hz : float, optional
}
class OpticalFilter {
<<DeviceModel>>
--------------------------------------
attributes
--------------------------------------
**filter_type** : text
}
class BandOpticalFilter {
<<OpticalFilter>>
--------------------------------------
attributes
--------------------------------------
**center_wavelength_in_nm** : float
**bandwidth_in_nm** : float
}
class EdgeOpticalFilter {
<<OpticalFilter>>
--------------------------------------
attributes
--------------------------------------
**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 DichroicMirror {
<<DeviceModel>>
--------------------------------------
attributes
--------------------------------------
cut_on_wavelength_in_nm : numeric, optional
cut_off_wavelength_in_nm : numeric, optional
reflection_band_in_nm : numeric, optional
transmission_band_in_nm : numeric, optional
angle_of_incidence_in_degrees : numeric, optional
}
class Photodetector {
<<DeviceModel>>
--------------------------------------
attributes
--------------------------------------
**detector_type** : text
**detected_wavelength_in_nm** : float
gain : float, optional
gain_unit : text, optional
}
class Indicator {
<<NWBContainer>>
--------------------------------------
attributes
--------------------------------------
**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
DeviceModel <|-- DichroicMirror : extends
ExcitationSource <|-- PulsedExcitationSource : extends
OpticalFilter <|-- BandOpticalFilter : extends
OpticalFilter <|-- EdgeOpticalFilter : extends
ExcitationLightPath o--> ExcitationSource : links
ExcitationLightPath o--> OpticalFilter : links
ExcitationLightPath o--> DichroicMirror : links
EmissionLightPath o--> Photodetector : links
EmissionLightPath o--> OpticalFilter : links
EmissionLightPath o--> DichroicMirror : links
EmissionLightPath *-- Indicator : contains
Illumination Pattern Components
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
classDiagram
direction TB
class IlluminationPattern {
<<NWBContainer>>
--------------------------------------
attributes
--------------------------------------
description : text, optional
}
class LineScan {
<<IlluminationPattern>>
--------------------------------------
attributes
--------------------------------------
scan_direction : text, optional
line_rate_in_Hz : float64, optional
dwell_time_in_s : float64, optional
}
class PlaneAcquisition {
<<IlluminationPattern>>
--------------------------------------
attributes
--------------------------------------
plane_thickness_in_um : float64, optional
illumination_angle_in_degrees : float64, optional
plane_rate_in_Hz : float64, optional
}
class RandomAccessScan {
<<IlluminationPattern>>
--------------------------------------
attributes
--------------------------------------
max_scan_points : numeric, optional
dwell_time_in_s : float64, optional
scanning_pattern : text, optional
}
class ImagingSpace {
<<NWBContainer>>
--------------------------------------
datasets
--------------------------------------
**description** : text
origin_coordinates : float64[3], optional
unit : text = "micrometers"
--------------------------------------
attributes
--------------------------------------
location : text, optional
reference_frame : text, optional
orientation : text, optional
--------------------------------------
groups
--------------------------------------
**illumination_pattern** : IlluminationPattern
}
IlluminationPattern <|-- LineScan : extends
IlluminationPattern <|-- PlaneAcquisition : extends
IlluminationPattern <|-- RandomAccessScan : extends
ImagingSpace *-- IlluminationPattern : contains
Microscopy Series and Imaging Space Components
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
classDiagram
direction TB
class MicroscopySeries {
<<TimeSeries>>
--------------------------------------
links
--------------------------------------
**microscope** : Microscope
**excitation_light_path** : ExcitationLightPath
**emission_light_path** : EmissionLightPath
}
class PlanarMicroscopySeries {
<<MicroscopySeries>>
--------------------------------------
datasets
--------------------------------------
**data** : numeric[frames, height, width]
--------------------------------------
groups
--------------------------------------
**imaging_space** : PlanarImagingSpace
}
class VolumetricMicroscopySeries {
<<MicroscopySeries>>
--------------------------------------
datasets
--------------------------------------
**data** : numeric[frames, height, width, depths]
--------------------------------------
groups
--------------------------------------
**imaging_space** : VolumetricImagingSpace
}
class MultiPlaneMicroscopyContainer {
<<NWBDataInterface>>
--------------------------------------
groups
--------------------------------------
**planar_microscopy_series** : PlanarMicroscopySeries[1..*]
}
class ImagingSpace {
<<NWBContainer>>
--------------------------------------
datasets
--------------------------------------
**description** : text
origin_coordinates : float64[3], optional
unit : text = "micrometers"
--------------------------------------
attributes
--------------------------------------
location : text, optional
reference_frame : text, optional
orientation : text, optional
--------------------------------------
groups
--------------------------------------
**illumination_pattern** : IlluminationPattern
}
class PlanarImagingSpace {
<<ImagingSpace>>
--------------------------------------
datasets
--------------------------------------
pixel_size_in_um : float64[2], optional
}
class VolumetricImagingSpace {
<<ImagingSpace>>
--------------------------------------
datasets
--------------------------------------
voxel_size_in_um : float64[3], optional
}
class Microscope {
<<Device>>
--------------------------------------
attributes
--------------------------------------
model : text, optional
technique : text, optional
}
MicroscopySeries <|-- PlanarMicroscopySeries : extends
MicroscopySeries <|-- VolumetricMicroscopySeries : extends
ImagingSpace <|-- PlanarImagingSpace : extends
ImagingSpace <|-- VolumetricImagingSpace : extends
PlanarMicroscopySeries *-- PlanarImagingSpace : contains
VolumetricMicroscopySeries *-- VolumetricImagingSpace : contains
MultiPlaneMicroscopyContainer *-- PlanarMicroscopySeries : contains
MicroscopySeries o--> Microscope : links
MicroscopySeries o--> ExcitationLightPath : links
MicroscopySeries o--> EmissionLightPath : links
Segmentation Components
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
classDiagram
direction TB
class Segmentation {
<<DynamicTable>>
--------------------------------------
attributes
--------------------------------------
**description** : text
--------------------------------------
groups
--------------------------------------
summary_images : SummaryImage[0..*]
}
class Segmentation2D {
<<Segmentation>>
--------------------------------------
datasets
--------------------------------------
image_mask : VectorData[num_roi, num_x, num_y], optional
pixel_mask_index : VectorIndex, optional
pixel_mask : VectorData, optional
--------------------------------------
groups
--------------------------------------
**imaging_space** : PlanarImagingSpace
--------------------------------------
methods
--------------------------------------
add_roi()
create_roi_table_region()
pixel_to_image()
image_to_pixel()
}
class Segmentation3D {
<<Segmentation>>
--------------------------------------
datasets
--------------------------------------
image_mask : VectorData[num_roi, num_x, num_y, num_z], optional
voxel_mask_index : VectorIndex, optional
voxel_mask : VectorData, optional
--------------------------------------
groups
--------------------------------------
**imaging_space** : VolumetricImagingSpace
--------------------------------------
methods
--------------------------------------
add_roi()
create_roi_table_region()
voxel_to_image()
image_to_voxel()
}
class SummaryImage {
<<NWBContainer>>
--------------------------------------
datasets
--------------------------------------
**data** : numeric[height, width] or numeric[height, width, depth]
--------------------------------------
attributes
--------------------------------------
**description** : text
}
class SegmentationContainer {
<<NWBDataInterface>>
--------------------------------------
groups
--------------------------------------
**segmentations** : Segmentation[1..*]
--------------------------------------
methods
--------------------------------------
add_segmentation()
}
class MicroscopyResponseSeries {
<<TimeSeries>>
--------------------------------------
datasets
--------------------------------------
**data** : numeric[number_of_frames, number_of_rois]
**rois** : DynamicTableRegion
}
class MicroscopyResponseSeriesContainer {
<<NWBDataInterface>>
--------------------------------------
groups
--------------------------------------
**microscopy_response_series** : MicroscopyResponseSeries[1..*]
}
Segmentation <|-- Segmentation2D : extends
Segmentation <|-- Segmentation3D : extends
SegmentationContainer *-- Segmentation : contains
Segmentation *-- SummaryImage : contains
MicroscopyResponseSeriesContainer *-- MicroscopyResponseSeries : contains
Segmentation2D *-- PlanarImagingSpace : contains
Segmentation3D *-- VolumetricImagingSpace : contains
This extension was created using ndx-template.
Installation
pip install ndx-microscopy
Documentation
For detailed documentation, including API reference and additional examples, please visit our documentation site.
Contributing
To help ensure a smooth Pull Request (PR) process, please always begin by raising an issue on the main repository so we can openly discuss any problems/additions before taking action.
The main branch of ndx-microscopy is protected; you cannot push to it directly. You must upload your changes by pushing a new branch, then submit your changes to the main branch via a Pull Request. This allows us to conduct automated testing of your contribution, and gives us a space for developers to discuss the contribution and request changes. If you decide to tackle an issue, please make yourself an assignee on the issue to communicate this to the team. Don’t worry - this does not commit you to solving this issue. It just lets others know who they should talk to about it.
From your local copy directory, use the following commands.
If you have not already, you will need to clone the repo:
$ git clone https://github.com/catalystneuro/ndx-microscopy
First create a new branch to work on
$ git checkout -b <new_branch>
Make your changes. Add new objects related to optical experiment or add more attributes on the existing ones. To speed up the process, you can write mock function (see _mock.py) that would be used to test the new neurodata type
We will automatically run tests to ensure that your contributions didn’t break anything and that they follow our style guide. You can speed up the testing cycle by running these tests locally on your own computer by calling pytest from the top-level directory. Push your feature branch to origin (i.e. GitHub)
$ git push origin <new_branch>
Once you have tested and finalized your changes, create a pull request (PR) targeting dev as the base branch: Ensure the PR description clearly describes the problem and solution. Include the relevant issue number if applicable. TIP: Writing e.g. “fix #613” will automatically close issue #613 when this PR is merged. Before submitting, please ensure that the code follows the standard coding style of the respective repository. If you would like help with your contribution, or would like to communicate contributions that are not ready to merge, submit a PR where the title begins with “[WIP].”
Update the CHANGELOG.md regularly to document changes to the extension.
License
MIT License. See LICENSE.txt for details.
