https://github.com/catalystneuro/ndx-microscopy - v0.2.1

v0.2.1 (March 28, 2025)

Bug Fixes

Fixed version in namespace YAML file and docs

- Python
Published by alessandratrapani about 1 year ago

https://github.com/catalystneuro/ndx-microscopy - v0.2.0

v0.2.0 (March 19, 2025)

Deprecations and Changes

• 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

Improvements

• 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

- Python
Published by alessandratrapani about 1 year ago

https://github.com/catalystneuro/ndx-microscopy - v0.1.0

Initial release of ndx-microscopy extension.

Features

• 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,Segmentation2D,Segmentation3D,SegmentationContainer,MicroscopyResponseSeries,MicroscopyResponseSeriesContainer
• Abstract Neurodata types: ImagingSpace, MicroscopySeries,Segmentation

Changes

• Initial implementation of all neurodata data types
• Basic documentation and examples
• Integration tests and validation

- Python
Published by alessandratrapani over 1 year ago