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CHANGELOG.md

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v0.3.0 (Jun 3, 2025)

Bug Fixes

Deprecations and Changes

  • Removed ExcitationLightPath and EmissionLightPath classes in favor of a more integrated approach with MicroscopyRig

Features

NWB TAB reviews Issue#48

  • Added MicroscopyChannel object Sub-Issue#49
  • Added MicroscopyRig object Sub-Issue#51
  • Changed Microscope to inherit from DeviceInstance instead of Device Sub-Issue#51
  • Added MicroscopeModel that inherit from DeviceModel Sub-Issue#51
  • Updated MicroscopySeries to use MicroscopyRig instead of individual microscope, excitation_light_path, and emission_light_path references Sub-Issue#51
  • Added dimensions_in_pixels to PlanarImagingSpace and dimensions_in_voxels to VolumetricImagingSpace object Sub-Issue#52
  • Added MultiChannelMicroscopyContainer object Sub-Issue#53
  • Refactored segmentation classes: Sub-Issue#56
    • Renamed Segmentation2D to PlanarSegmentation
    • Renamed Segmentation3D to VolumetricSegmentation
  • Added get_FOV_size() method to both PlanarImagingSpace and VolumetricImagingSpace classes for calculating Field of View size in micrometers Sub-Issue#53
  • Added microscopy_series link to MicroscopyResponseSeries class Sub-Issue#58
  • Changed image_to_voxel in volume_to_voxel, voxel_to_image in voxel_to_volume, and image_mask in volume_mask in VolumetricSegmentation Sub-Issue#57

v0.2.1 (March 28, 2025)

Bug Fixes

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