.. _api:

***
API
***

This section provides detailed documentation for all classes and methods in the ndx-microscopy extension.

Device Components
===========

MicroscopeModel
---------------
.. autoclass:: ndx_microscopy.MicroscopeModel
   :members:
   :undoc-members:
   :show-inheritance:

Microscope
---------
.. autoclass:: ndx_microscopy.Microscope
   :members:
   :undoc-members:
   :show-inheritance:

MicroscopyRig
-------------
.. autoclass:: ndx_microscopy.MicroscopyRig
   :members:
   :undoc-members:
   :show-inheritance:

MicroscopyChannel
---------------
.. autoclass:: ndx_microscopy.MicroscopyChannel
   :members:
   :undoc-members:
   :show-inheritance:

Illumination Pattern Components
==========================

IlluminationPattern
----------------
.. autoclass:: ndx_microscopy.IlluminationPattern
   :members:
   :undoc-members:
   :show-inheritance:

LineScan
-------
.. autoclass:: ndx_microscopy.LineScan
   :members:
   :undoc-members:
   :show-inheritance:

PlaneAcquisition
--------------
.. autoclass:: ndx_microscopy.PlaneAcquisition
   :members:
   :undoc-members:
   :show-inheritance:

RandomAccessScan
--------------
.. autoclass:: ndx_microscopy.RandomAccessScan
   :members:
   :undoc-members:
   :show-inheritance:

Imaging Space Components
=====================

ImagingSpace
-----------
.. autoclass:: ndx_microscopy.ImagingSpace
   :members:
   :undoc-members:
   :show-inheritance:

PlanarImagingSpace
-----------------
.. autoclass:: ndx_microscopy.PlanarImagingSpace
   :members:
   :undoc-members:
   :show-inheritance:

Methods
^^^^^^^
.. automethod:: ndx_microscopy.PlanarImagingSpace.get_FOV_size
VolumetricImagingSpace
---------------------
.. autoclass:: ndx_microscopy.VolumetricImagingSpace
   :members:
   :undoc-members:
   :show-inheritance:
   
Methods
^^^^^^^
.. automethod:: ndx_microscopy.VolumetricImagingSpace.get_FOV_size

Microscopy Series Components
=========================

MicroscopySeries
---------------
.. autoclass:: ndx_microscopy.MicroscopySeries
   :members:
   :undoc-members:
   :show-inheritance:

PlanarMicroscopySeries
---------------------
.. autoclass:: ndx_microscopy.PlanarMicroscopySeries
   :members:
   :undoc-members:
   :show-inheritance:

VolumetricMicroscopySeries
-------------------------
.. autoclass:: ndx_microscopy.VolumetricMicroscopySeries
   :members:
   :undoc-members:
   :show-inheritance:

MultiPlaneMicroscopyContainer
---------------------------
.. autoclass:: ndx_microscopy.MultiPlaneMicroscopyContainer
   :members:
   :undoc-members:
   :show-inheritance:

Segmentation Components
====================

Segmentation
-----------
.. autoclass:: ndx_microscopy.Segmentation
   :members:
   :undoc-members:
   :show-inheritance:

PlanarSegmentation
-------------
.. autoclass:: ndx_microscopy.PlanarSegmentation
   :members:
   :undoc-members:
   :show-inheritance:

Methods
^^^^^^^
.. automethod:: ndx_microscopy.PlanarSegmentation.add_roi
.. automethod:: ndx_microscopy.PlanarSegmentation.pixel_to_image
.. automethod:: ndx_microscopy.PlanarSegmentation.image_to_pixel
.. automethod:: ndx_microscopy.PlanarSegmentation.create_roi_table_region

VolumetricSegmentation
-------------
.. autoclass:: ndx_microscopy.VolumetricSegmentation
   :members:
   :undoc-members:
   :show-inheritance:

Methods
^^^^^^^
.. automethod:: ndx_microscopy.VolumetricSegmentation.add_roi
.. automethod:: ndx_microscopy.VolumetricSegmentation.voxel_to_volume
.. automethod:: ndx_microscopy.VolumetricSegmentation.volume_to_voxel
.. automethod:: ndx_microscopy.VolumetricSegmentation.create_roi_table_region

SegmentationContainer
-------------------
.. autoclass:: ndx_microscopy.SegmentationContainer
   :members:
   :undoc-members:
   :show-inheritance:

Methods
^^^^^^^
.. automethod:: ndx_microscopy.SegmentationContainer.add_segmentation

SummaryImage
-----------
.. autoclass:: ndx_microscopy.SummaryImage
   :members:
   :undoc-members:
   :show-inheritance:

Response Series Components
=======================

MicroscopyResponseSeries
----------------------
.. autoclass:: ndx_microscopy.MicroscopyResponseSeries
   :members:
   :undoc-members:
   :show-inheritance:

MicroscopyResponseSeriesContainer
------------------------------
.. autoclass:: ndx_microscopy.MicroscopyResponseSeriesContainer
   :members:
   :undoc-members:
   :show-inheritance: