Revise documentation structure and enhance descriptions for microscopy components

Author: alessandratrapani

docs/source/api.rst

@@ -6,140 +6,166 @@ API
 
 This section provides detailed documentation for all classes and methods in the ndx-microscopy extension.
 
-Microscope
-=========
+Device Components
+===========
 
+Microscope
+---------
 .. autoclass:: ndx_microscopy.Microscope
    :members:
    :undoc-members:
    :show-inheritance:
 
-Light Paths
-==========
+Light Path Components
+===================
 
 ExcitationLightPath
 ------------------
-
 .. autoclass:: ndx_microscopy.ExcitationLightPath
    :members:
    :undoc-members:
    :show-inheritance:
 
+Methods
+^^^^^^^
+.. automethod:: ndx_microscopy.ExcitationLightPath.get_excitation_wavelength
+
 EmissionLightPath
 ----------------
-
 .. autoclass:: ndx_microscopy.EmissionLightPath
    :members:
    :undoc-members:
    :show-inheritance:
 
-Imaging Spaces
-=============
+Methods
+^^^^^^^
+.. automethod:: ndx_microscopy.EmissionLightPath.get_emission_wavelength
+.. automethod:: ndx_microscopy.EmissionLightPath.get_indicator_label
+
+Imaging Space Components
+=====================
 
 ImagingSpace
 -----------
-
 .. autoclass:: ndx_microscopy.ImagingSpace
    :members:
    :undoc-members:
    :show-inheritance:
 
 PlanarImagingSpace
 -----------------
-
 .. autoclass:: ndx_microscopy.PlanarImagingSpace
    :members:
    :undoc-members:
    :show-inheritance:
 
 VolumetricImagingSpace
 ---------------------
-
 .. autoclass:: ndx_microscopy.VolumetricImagingSpace
    :members:
    :undoc-members:
    :show-inheritance:
 
-Microscopy Series
-================
+Microscopy Series Components
+=========================
 
 MicroscopySeries
 ---------------
-
 .. autoclass:: ndx_microscopy.MicroscopySeries
    :members:
    :undoc-members:
    :show-inheritance:
 
 PlanarMicroscopySeries
 ---------------------
-
 .. autoclass:: ndx_microscopy.PlanarMicroscopySeries
    :members:
    :undoc-members:
    :show-inheritance:
 
-VariableDepthMicroscopySeries
-----------------------------
+VolumetricMicroscopySeries
+-------------------------
+.. autoclass:: ndx_microscopy.VolumetricMicroscopySeries
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-.. autoclass:: ndx_microscopy.VariableDepthMicroscopySeries
+MultiPlaneMicroscopyContainer
+---------------------------
+.. autoclass:: ndx_microscopy.MultiPlaneMicroscopyContainer
    :members:
    :undoc-members:
    :show-inheritance:
 
-VolumetricMicroscopySeries
--------------------------
+Segmentation Components
+====================
 
-.. autoclass:: ndx_microscopy.VolumetricMicroscopySeries
+Segmentation
+-----------
+.. autoclass:: ndx_microscopy.Segmentation
    :members:
    :undoc-members:
    :show-inheritance:
 
-Multi-Channel Data
-================
+Segmentation2D
+-------------
+.. autoclass:: ndx_microscopy.Segmentation2D
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-MultiChannelMicroscopyVolume
----------------------------
+Methods
+^^^^^^^
+.. automethod:: ndx_microscopy.Segmentation2D.add_roi
+.. automethod:: ndx_microscopy.Segmentation2D.pixel_to_image
+.. automethod:: ndx_microscopy.Segmentation2D.image_to_pixel
+.. automethod:: ndx_microscopy.Segmentation2D.create_roi_table_region
 
-.. autoclass:: ndx_microscopy.MultiChannelMicroscopyVolume
+Segmentation3D
+-------------
+.. autoclass:: ndx_microscopy.Segmentation3D
    :members:
    :undoc-members:
    :show-inheritance:
 
-VariableDepthMultiChannelMicroscopyVolume
----------------------------------------
+Methods
+^^^^^^^
+.. automethod:: ndx_microscopy.Segmentation3D.add_roi
+.. automethod:: ndx_microscopy.Segmentation3D.voxel_to_image
+.. automethod:: ndx_microscopy.Segmentation3D.image_to_voxel
+.. automethod:: ndx_microscopy.Segmentation3D.create_roi_table_region
 
-.. autoclass:: ndx_microscopy.VariableDepthMultiChannelMicroscopyVolume
+SegmentationContainer
+-------------------
+.. autoclass:: ndx_microscopy.SegmentationContainer
    :members:
    :undoc-members:
    :show-inheritance:
 
-Response Data
-============
+Methods
+^^^^^^^
+.. automethod:: ndx_microscopy.SegmentationContainer.add_segmentation
 
-MicroscopyResponseSeries
------------------------
-
-.. autoclass:: ndx_microscopy.MicroscopyResponseSeries
+SummaryImage
+-----------
+.. autoclass:: ndx_microscopy.SummaryImage
    :members:
    :undoc-members:
    :show-inheritance:
 
-Segmentation
-===========
+Response Series Components
+=======================
 
-MicroscopySegmentations
+MicroscopyResponseSeries
 ----------------------
-
-.. autoclass:: ndx_microscopy.MicroscopySegmentations
+.. autoclass:: ndx_microscopy.MicroscopyResponseSeries
    :members:
    :undoc-members:
    :show-inheritance:
 
-MicroscopyPlaneSegmentation
---------------------------
-
-.. autoclass:: ndx_microscopy.MicroscopyPlaneSegmentation
+MicroscopyResponseSeriesContainer
+------------------------------
+.. autoclass:: ndx_microscopy.MicroscopyResponseSeriesContainer
    :members:
    :undoc-members:
    :show-inheritance: