Release Notes¶

Version 0.3.0 (Jun 3, 2025)¶

Removed ExcitationLightPath and EmissionLightPath classes in favor of a more integrated approach with MicroscopyRig
Changed Microscope to inherit from DeviceInstance instead of Device
Updated MicroscopySeries to use MicroscopyRig instead of individual microscope, excitation_light_path, and emission_light_path references
Refactored segmentation classes: * Renamed Segmentation2D to PlanarSegmentation * Renamed Segmentation3D to VolumetricSegmentation
Changed image_to_voxel in volume_to_voxel
Changed voxel_to_image in voxel_to_volume
Changed image_mask in volume_mask in VolumetricSegmentation

Added MicroscopeModel class to define microscope models (inherits from DeviceModel)
Added MicroscopyRig class to organize all optical components in a single container, including: * microscope: Link to the Microscope instance * excitation_source: Link to ExcitationSource (optional) * excitation_filter: Link to OpticalFilter (optional) * dichroic_mirror: Link to DichroicMirror (optional) * photodetector: Link to Photodetector (optional) * emission_filter: Link to OpticalFilter (optional)
Added MicroscopyChannel class to represent a single channel in a microscopy series, which includes: * excitation_wavelength: Excitation wavelength for the channel * emission_wavelength: Emission wavelength for the channel * indicator: Link to Indicator
Added MultiChannelMicroscopyContainer class to support multi-channel imaging data. * This class allows for the storage of multiple MicroscopySeries objects, each representing a different channel of imaging data. * It provides methods to access and manipulate individual channels, facilitating the analysis of multi-channel datasets.
Added dimensions_in_pixels to PlanarImagingSpace and dimensions_in_voxels to VolumetricImagingSpace
Added get_FOV_size() method to both PlanarImagingSpace and VolumetricImagingSpace classes for calculating Field of View size in micrometers
Added microscopy_series link to MicroscopyResponseSeries class to point the MicroscopySeries this response series is derived from.

Simplified the optical path configuration by consolidating components into a single MicroscopyRig container
Improved organization of device components with the addition of MicroscopeModel and clearer inheritance structure
Updated all documentation and examples to reflect the new structure

These changes are NOT backward compatible and require updating existing code to use the new structure
The MicroscopyRig approach provides a more flexible and intuitive way to organize optical components
Improved organization of multi channel imaging data

Change grid_spacing_in_um in pixel_size_in_um and voxel_size_in_um (and relative doc string) to better represent the physical dimension of the fundamental unit of the image (pixel or voxel).

## Bug Fixes

## Features

New illumination pattern classes to represent different microscopy scanning methods: * IlluminationPattern: Base class for describing the illumination pattern used to acquire images * LineScan: Line scanning method commonly used in two-photon microscopy * PlaneAcquisition: Whole plane acquisition method, common for light sheet and one-photon techniques * RandomAccessScan: Random access method for targeted, high-speed imaging of specific regions
Added technique attribute to the Microscope class to describe the imaging technique used
Updated ImagingSpace classes to include an illumination_pattern parameter, creating a direct link between the imaging space and the acquisition method
Added mock implementations for all new classes in _mock.py for testing purposes
Updated example notebooks to demonstrate the use of different scanning methods

Notes

These changes are backward compatible and add new functionality without removing existing features
The illumination_pattern parameter is now required when creating ImagingSpace objects

Initial release of ndx-microscopy extension.

Microscope metadata: Microscope
Integration with ndx-ophys-devices for optical component specifications: ExcitationSource/PulsedExcitationSource, BandOpticalFilter/EdgeOpticalFilter, DichroicMirror, Photodetector, Indicator
Advanced light path configurations: ExcitationLightPath, EmissionLightPath
Imaging space definitions: PlanarImagingSpace, VolumetricImagingSpace
Support for 2D and 3D imaging: PlanarMicroscopySeries, VolumetricMicroscopySeries, MultiPlaneMicroscopyContainer
ROI/segmentation storage: SummaryImages, PlanarSegmentation, VolumetricSegmentation, SegmentationContainer, MicroscopyResponseSeries, MicroscopyResponseSeriesContainer
Abstract Neurodata types: ImagingSpace, MicroscopySeries, Segmentation