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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
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‎CHANGELOG.md‎

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- Updated `MicroscopySeries` to use `MicroscopyRig` instead of individual `microscope`, `excitation_light_path`, and `emission_light_path` references Sub-Issue[#51](https://github.com/catalystneuro/ndx-microscopy/issues/51)
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- Added `dimensions_in_pixels` to `PlanarImagingSpace` and `dimensions_in_voxels` to `VolumetricImagingSpace` object Sub-Issue[#52](https://github.com/catalystneuro/ndx-microscopy/issues/52)
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- Added `MultiChannelMicroscopyContainer` object Sub-Issue[#53](https://github.com/catalystneuro/ndx-microscopy/issues/53)
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- Refactored segmentation classes: Sub-Issue[#56](https://github.com/catalystneuro/ndx-microscopy/issues/56)
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- Renamed `Segmentation2D` to `PlanarSegmentation`
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- Renamed `Segmentation3D` to `VolumetricSegmentation`
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# v0.2.1 (March 28, 2025)
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‎README.md‎

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@@ -30,8 +30,8 @@ A Neurodata Without Borders (NWB) extension for storing microscopy data and asso
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- `MultiPlaneMicroscopyContainer`
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- `MultiChannelMicroscopyContainer`
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- ROI/segmentation storage:
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- `Segmentation2D`
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- `Segmentation3D`
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- `PlanarSegmentation`
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- `VolumetricSegmentation`
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- `SegmentationContainer`
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- `MicroscopyResponseSeries`
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- `MicroscopyResponseSeriesContainer`
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summary_images : SummaryImage[0..*]
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}
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class Segmentation2D {
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class PlanarSegmentation {
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<<Segmentation>>
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--------------------------------------
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datasets
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image_to_pixel()
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}
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class Segmentation3D {
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class VolumetricSegmentation {
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<<Segmentation>>
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--------------------------------------
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datasets
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**microscopy_response_series** : MicroscopyResponseSeries[1..*]
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}
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Segmentation <|-- Segmentation2D : extends
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Segmentation <|-- Segmentation3D : extends
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Segmentation <|-- PlanarSegmentation : extends
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Segmentation <|-- VolumetricSegmentation : extends
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SegmentationContainer *-- Segmentation : contains
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Segmentation *-- SummaryImage : contains
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MicroscopyResponseSeriesContainer *-- MicroscopyResponseSeries : contains
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Segmentation2D *-- PlanarImagingSpace : contains
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Segmentation3D *-- VolumetricImagingSpace : contains
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PlanarSegmentation *-- PlanarImagingSpace : contains
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VolumetricSegmentation *-- VolumetricImagingSpace : contains
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```
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---

‎docs/source/api.rst‎

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:undoc-members:
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:show-inheritance:
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Segmentation2D
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PlanarSegmentation
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-------------
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.. autoclass:: ndx_microscopy.Segmentation2D
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.. autoclass:: ndx_microscopy.PlanarSegmentation
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:members:
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:undoc-members:
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:show-inheritance:
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Methods
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^^^^^^^
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.. automethod:: ndx_microscopy.Segmentation2D.add_roi
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.. automethod:: ndx_microscopy.Segmentation2D.pixel_to_image
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.. automethod:: ndx_microscopy.Segmentation2D.image_to_pixel
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.. automethod:: ndx_microscopy.Segmentation2D.create_roi_table_region
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.. automethod:: ndx_microscopy.PlanarSegmentation.add_roi
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.. automethod:: ndx_microscopy.PlanarSegmentation.pixel_to_image
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.. automethod:: ndx_microscopy.PlanarSegmentation.image_to_pixel
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.. automethod:: ndx_microscopy.PlanarSegmentation.create_roi_table_region
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Segmentation3D
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VolumetricSegmentation
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-------------
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.. autoclass:: ndx_microscopy.Segmentation3D
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.. autoclass:: ndx_microscopy.VolumetricSegmentation
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:members:
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:undoc-members:
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:show-inheritance:
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Methods
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^^^^^^^
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.. automethod:: ndx_microscopy.Segmentation3D.add_roi
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.. automethod:: ndx_microscopy.Segmentation3D.voxel_to_image
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.. automethod:: ndx_microscopy.Segmentation3D.image_to_voxel
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.. automethod:: ndx_microscopy.Segmentation3D.create_roi_table_region
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.. automethod:: ndx_microscopy.VolumetricSegmentation.add_roi
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.. automethod:: ndx_microscopy.VolumetricSegmentation.voxel_to_image
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.. automethod:: ndx_microscopy.VolumetricSegmentation.image_to_voxel
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.. automethod:: ndx_microscopy.VolumetricSegmentation.create_roi_table_region
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SegmentationContainer
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-------------------

‎docs/source/examples.rst‎

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MicroscopyChannel,
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PlanarImagingSpace,
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PlanarMicroscopySeries,
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Segmentation2D,
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PlanarSegmentation,
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SummaryImage,
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MicroscopyResponseSeries,
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MicroscopyResponseSeriesContainer,
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)
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# Create segmentation
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segmentation = Segmentation2D(
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segmentation = PlanarSegmentation(
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name='rois',
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description='Manual ROI segmentation',
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planar_imaging_space=imaging_space,
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MicroscopyRig,
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VolumetricImagingSpace,
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VolumetricMicroscopySeries,
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Segmentation3D,
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VolumetricSegmentation,
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SummaryImage,
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MicroscopyResponseSeries,
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MicroscopyResponseSeriesContainer,
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)
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# Create 3D segmentation
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segmentation = Segmentation3D(
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segmentation = VolumetricSegmentation(
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name='volume_rois',
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description='3D ROI segmentation',
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volumetric_imaging_space=volume_space,
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PlanarImagingSpace,
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PlanarMicroscopySeries,
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MultiPlaneMicroscopyContainer,
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Segmentation2D,
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PlanarSegmentation,
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SummaryImage,
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MicroscopyResponseSeries,
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MicroscopyResponseSeriesContainer,
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)
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# Create segmentation for this plane
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segmentation = Segmentation2D(
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segmentation = PlanarSegmentation(
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name=f'rois_{depth}',
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description=f'ROI segmentation at {depth} µm',
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planar_imaging_space=plane_space,

‎docs/source/format.rst‎

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doc: Summary images that are related to the segmentation, e.g., mean, correlation, maximum projection.
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quantity: "*"
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Segmentation2D
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PlanarSegmentation
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^^^^^^^^^^^
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For 2D segmentation data.
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.. code-block:: yaml
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groups:
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- neurodata_type_def: Segmentation2D
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- neurodata_type_def: PlanarSegmentation
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neurodata_type_inc: Segmentation
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doc: Results from image segmentation of a specific planar imaging space.
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datasets:
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- neurodata_type_inc: PlanarImagingSpace
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doc: PlanarImagingSpace object from which this data was generated.
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Segmentation3D
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VolumetricSegmentation
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^^^^^^^^^^^
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For 3D segmentation data.
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.. code-block:: yaml
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- neurodata_type_def: Segmentation3D
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- neurodata_type_def: VolumetricSegmentation
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neurodata_type_inc: Segmentation
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doc: Results from image segmentation of a specific volumetric imaging space.
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datasets:

‎docs/source/release_notes.rst‎

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* Removed `ExcitationLightPath` and `EmissionLightPath` classes in favor of a more integrated approach with `MicroscopyRig`
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* Changed `Microscope` to inherit from `DeviceInstance` instead of `Device`
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* Updated `MicroscopySeries` to use `MicroscopyRig` instead of individual `microscope`, `excitation_light_path`, and `emission_light_path` references
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* Refactored segmentation classes:
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* Renamed ``Segmentation2D`` to ``PlanarSegmentation``
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* Renamed ``Segmentation3D`` to ``VolumetricSegmentation``
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Features
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--------
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* Advanced light path configurations: ``ExcitationLightPath``, ``EmissionLightPath``
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* Imaging space definitions: ``PlanarImagingSpace``, ``VolumetricImagingSpace``
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* Support for 2D and 3D imaging: ``PlanarMicroscopySeries``, ``VolumetricMicroscopySeries``, ``MultiPlaneMicroscopyContainer``
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* ROI/segmentation storage: ``SummaryImages``, ``Segmentation2D``, ``Segmentation3D``, ``SegmentationContainer``, ``MicroscopyResponseSeries``, ``MicroscopyResponseSeriesContainer``
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* ROI/segmentation storage: ``SummaryImages``, ``PlanarSegmentation``, ``VolumetricSegmentation``, ``SegmentationContainer``, ``MicroscopyResponseSeries``, ``MicroscopyResponseSeriesContainer``
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* Abstract Neurodata types: ``ImagingSpace``, ``MicroscopySeries``, ``Segmentation``
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Changes

‎docs/source/user_guide.rst‎

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# 2. Create segmentation
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segmentation = Segmentation2D(
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segmentation = PlanarSegmentation(
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‎examples/multi_plane_imaging_example.ipynb‎

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" PlanarImagingSpace,\n",
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" PlanarMicroscopySeries,\n",
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" MultiPlaneMicroscopyContainer,\n",
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" Segmentation2D,\n",
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" PlanarSegmentation,\n",
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" SummaryImage,\n",
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" MicroscopyResponseSeries,\n",
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" )\n",
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"\n",
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" # Create segmentation for this plane\n",
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" segmentation = Segmentation2D(\n",
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" segmentation = PlanarSegmentation(\n",
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" name=f\"rois_{depth}\",\n",
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" description=f\"ROI segmentation at {depth} µm\",\n",
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" planar_imaging_space=plane_space,\n",

‎examples/one-photon_calcium_imaging_example.ipynb‎

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" MicroscopyChannel,\n",
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" PlanarImagingSpace,\n",
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" PlanarMicroscopySeries,\n",
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" Segmentation2D,\n",
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" PlanarSegmentation,\n",
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" SummaryImage,\n",
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" MicroscopyResponseSeries,\n",
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" MicroscopyResponseSeriesContainer,\n",
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")\n",
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"\n",
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"# Create segmentation\n",
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"segmentation = Segmentation2D(\n",
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"segmentation = PlanarSegmentation(\n",
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" description='Manual ROI segmentation',\n",
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" planar_imaging_space=imaging_space,\n",

‎examples/two-photon_calcium_imaging_example.ipynb‎

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" LineScan,\n",
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" Segmentation2D,\n",
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" PlanarSegmentation,\n",
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")\n",
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"\n",
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"segmentation = Segmentation2D(\n",
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"segmentation = PlanarSegmentation(\n",
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" name='rois',\n",
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" description='Manual ROI segmentation',\n",
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" planar_imaging_space=imaging_space,\n",

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