Update documentation

Author: alessandratrapani

README.md

@@ -18,6 +18,11 @@ A Neurodata Without Borders (NWB) extension for storing microscopy data and asso
 - Imaging space definitions: 
     - `PlanarImagingSpace`
     - `VolumetricImagingSpace`
+- Illumination pattern classes:
+    - `IlluminationPattern`
+    - `LineScan`
+    - `PlaneAcquisition`
+    - `RandomAccessScan`
 - Support for 2D and 3D imaging: 
     - `PlanarMicroscopySeries`
     - `VolumetricMicroscopySeries`
@@ -192,6 +197,78 @@ classDiagram
     EmissionLightPath *-- Indicator : contains
 ```
 
+#### Illumination Pattern Components
+
+```mermaid
+%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
+
+classDiagram
+    direction TB
+
+    class IlluminationPattern {
+        <<NWBContainer>>
+        --------------------------------------
+        attributes
+        --------------------------------------
+        description : text, optional
+    }
+
+    class LineScan {
+        <<IlluminationPattern>>
+        --------------------------------------
+        attributes
+        --------------------------------------
+        scan_direction : text, optional
+        line_rate_in_Hz : float64, optional
+        dwell_time_in_s : float64, optional
+    }
+
+    class PlaneAcquisition {
+        <<IlluminationPattern>>
+        --------------------------------------
+        attributes
+        --------------------------------------
+        plane_thickness_in_um : float64, optional
+        illumination_angle_in_degrees : float64, optional
+        plane_rate_in_Hz : float64, optional
+    }
+
+    class RandomAccessScan {
+        <<IlluminationPattern>>
+        --------------------------------------
+        attributes
+        --------------------------------------
+        max_scan_points : numeric, optional
+        dwell_time_in_s : float64, optional
+        scanning_pattern : text, optional
+    }
+
+    class ImagingSpace {
+        <<NWBContainer>>
+        --------------------------------------
+        datasets
+        --------------------------------------
+        **description** : text
+        origin_coordinates : float64[3], optional
+        unit : text = "micrometers"
+        --------------------------------------
+        attributes
+        --------------------------------------
+        location : text, optional
+        reference_frame : text, optional
+        orientation : text, optional
+        --------------------------------------
+        groups
+        --------------------------------------
+        **illumination_pattern** : IlluminationPattern
+    }
+
+    IlluminationPattern <|-- LineScan : extends
+    IlluminationPattern <|-- PlaneAcquisition : extends
+    IlluminationPattern <|-- RandomAccessScan : extends
+    ImagingSpace *-- IlluminationPattern : contains
+```
+
 #### Microscopy Series and Imaging Space Components
 
 ```mermaid
@@ -256,6 +333,10 @@ classDiagram
         location : text, optional
         reference_frame : text, optional
         orientation : text, optional
+        --------------------------------------
+        groups
+        --------------------------------------
+        **illumination_pattern** : IlluminationPattern
     }
 
     class PlanarImagingSpace {
@@ -280,6 +361,7 @@ classDiagram
         attributes
         --------------------------------------
         model : text, optional
+        technique : text, optional
     }
 
     MicroscopySeries <|-- PlanarMicroscopySeries : extends

docs/source/description.rst

@@ -5,16 +5,6 @@ Overview
 
 The ndx-microscopy extension for NWB provides a standardized way to store and organize microscopy data in neuroscience research. This extension integrates with `ndx-ophys-devices <https://github.com/catalystneuro/ndx-ophys-devices>`_ to provide comprehensive optical component specifications and supports various microscopy techniques while maintaining detailed metadata about the imaging setup, experimental conditions, and acquired data.
 
-Supported Microscopy Techniques
------------------------------
-
-1. One-photon Microscopy (Widefield)
-2. Two-photon Microscopy
-3. Three-photon Microscopy
-4. Light Sheet Microscopy
-
-For support of additional techniques, please open an issue on `GitHub <https://github.com/catalystneuro/ndx-microscopy/issues>`_.
-
 Key Features
 ----------
 
@@ -35,13 +25,22 @@ Light Path Configuration
 - Comprehensive optical component specifications
 - Wavelength and power specifications
 
+Illumination Pattern Support
+^^^^^^^^^^^^^^^^^^^^^
+- Base illumination pattern class for general use cases
+- Line scanning for high-speed XY raster scanning acquisition
+- Plane acquisition for light sheet and widefield techniques
+- Random access scanning for targeted region imaging
+- Detailed scanning parameters (rates, directions, dwell times)
+
 Imaging Space Management
 ^^^^^^^^^^^^^^^^^^^^^
 - 2D planar imaging spaces
 - 3D volumetric imaging spaces
 - Precise coordinate system handling
 - Reference frame management
 - Grid spacing and resolution tracking
+- Integration with illumination patterns
 
 Data Organization
 ^^^^^^^^^^^^^

docs/source/release_notes.rst

@@ -4,6 +4,39 @@
 Release Notes
 *************
 
+Version 0.2.0 (Upcoming)
+============
+
+Added support for different microscopy scanning methods and improved metadata.
+
+Added
+--------
+
+* 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
+
+Changed
+-------
+
+* Modified the YAML specification to include new neurodata type definitions and relationships
+* Updated Python implementation files to expose the new classes in the API
+* Enhanced test files to verify the new classes work correctly
+
+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
+
 Version 0.1.0
 ============
 
@@ -12,13 +45,13 @@ Initial release of ndx-microscopy extension.
 Features
 --------
 
-* Microscope metadata: `Microscope`
-* Integration with ndx-ophys-devices for optical component specifications: `ExcitationSource`/`PulsedExcitationSource`,`BandOpticalFilter`/`EdgeOpticalFilter`,`DichroicMirror`,`Photodetector`,`Indicator`
-* Advanced light path configurations: `ExcitationLightPath`,`EmissionLightPath` 
-* Imaging space definitions: `PlanarImagingSpace`,`VolumetricImagingSpace`
-* Support for 2D and 3D imaging: `PlanarMicroscopySeries`,`VolumetricMicroscopySeries`,`MultiPlaneMicroscopyContainer`
-* ROI/segmentation storage: `SummaryImages`,`Segmentation2D`,`Segmentation3D`,`SegmentationContainer`,`MicroscopyResponseSeries`,`MicroscopyResponseSeriesContainer`
-* Abstract Neurodata types: `ImagingSpace`, `MicroscopySeries`,`Segmentation`
+* Microscope metadata: ``Microscope``
+* Integration with ndx-ophys-devices for optical component specifications: ``ExcitationSource``/``PulsedExcitationSource``, ``BandOpticalFilter``/``EdgeOpticalFilter``, ``DichroicMirror``, ``Photodetector``, ``Indicator``
+* Advanced light path configurations: ``ExcitationLightPath``, ``EmissionLightPath`` 
+* Imaging space definitions: ``PlanarImagingSpace``, ``VolumetricImagingSpace``
+* Support for 2D and 3D imaging: ``PlanarMicroscopySeries``, ``VolumetricMicroscopySeries``, ``MultiPlaneMicroscopyContainer``
+* ROI/segmentation storage: ``SummaryImages``, ``Segmentation2D``, ``Segmentation3D``, ``SegmentationContainer``, ``MicroscopyResponseSeries``, ``MicroscopyResponseSeriesContainer``
+* Abstract Neurodata types: ``ImagingSpace``, ``MicroscopySeries``, ``Segmentation``
 
 Changes
 -------