Switch image with volume in VolumetricSegmentation#67
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alessandratrapani merged 9 commits intov0.3.xfrom Jun 3, 2025
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* Add MicroscopyChannel object (#59) * add MicroscopyChannel to namespace * add mock function for MicroscopyChannel * update tests * update README * update docs * update notebooks * update changelog * Update PlaneAcquisition attribute from plane_thickness_in_um to point_spread_function_in_um across documentation and tests (#60) * Add Microscopy Rig (#61) * add MicroscopyRig and MicroscopeModel * add mock functions * update tests * update README * update docs * update notebooks * update changelog * ruff fixes * update requirements * update ndx-ophys-devices dependency to use GitHub repository * update ndx-ophys-devices dependency to version 0.2.0 and add OpticalLens to the namespace and extensions * update ndx-ophys-devices dependency to version 0.2.0 and add OpticalLens to the namespace and extensions * Update release notes for version 0.3.0 to reflect accurate date and added features * Add dimension attribute to ImagingSpace (#62) * add dimensions_in_pixels and dimensions_in_voxels * update mock functions * update README * update docs * update notebooks * update changelog * Add MultiChannelMicroscopyContainer (#63) * Add MultiChannelMicroscopyContainer and related tests to ndx-microscopy extension * update README * update CHANGELOG * update documentation * Refactor multi-channel microscopy container tests to use mock_MicroscopyRig and mock_MicroscopyChannel * ruff fix * Rename Segmentation2D to PlanarSegmentation and Segmentation3D to VolumetricSegmentation (#64) * Refactor segmentation classes: Rename Segmentation2D to PlanarSegmentation and Segmentation3D to VolumetricSegmentation * Update release notes and changelog for version 0.3.0: document segmentation class refactor * Add get_FOV_size() (#65) * add dimensions_in_pixels and dimensions_in_voxels * update mock functions * update README * update docs * update notebooks * update changelog * Add FOV size calculation methods for Planar and Volumetric Imaging Spaces * Fix pixel_size_in_um type in mock_PlanarImagingSpace function * Add tests for FOV size calculations * update README * update CHANGELOG * update docs * Optional link in MicroscopyResponseSeries to MicroscopySeries (#66) * Add link to MicroscopySeries in MicroscopyResponseSeries documentation * Add optional parameter to mock_MicroscopyResponseSeries for better testing flexibility * Add test for MicroscopyResponseSeries with associated MicroscopySeries * update README * update notebooks * update docs * update CHANGELOG * fix tests failure * Refactor microscopy response series tests to use updated mock objects * Switch image with volume in VolumetricSegmentation (#67) * Rename image_mask to volume_mask * Rename image_mask to volume_mask in Segmentation3D API and update related methods * Rename image_shape to volume_shape and update related references in mock_Segmentation3D * Rename image_mask to volume_mask in volumetric segmentation tests and update related assertions * update README * update notebook * update docs * Update CHANGELOG * minor fixes * Bump version to 0.3.0 in pyproject.toml and ndx-microscopy.namespace.yaml * Update project version to 0.3.0 and standardize string formatting in conf.py
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Fix #57
image_maskinvolume_maskin Segmentation3Dimage_to_voxelinvolume_to_voxelandvoxel_to_imageinvoxel_to_volume