initial setup

.gitignore

@@ -114,3 +114,6 @@ venv.bak/
 
 # Mac finder
 .DS_Store
+
+# PyCharm
+.idea/

README.md

@@ -1,14 +1,188 @@
 # ndx-microscopy Extension for NWB
 
-Description of the extension
+An enhancement to core NWB schema types related to microscopy data.
+
+Planned for an eventual NWBEP with the TAB.
+
 
 ## Installation
 
+```
+git clone https://github.com/catalystneuro/ndx-microscopy
+pip install ndx-microscopy
+```
+
 
 ## Usage
 
 ```python
+# TODO
+```
+
+
+## Entity relationship diagram
+
+```mermaid
+%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', "primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
+
+
+classDiagram
+    direction LR
+
+    class MicroscopySeries {
+        <<TimeSeries>>
+
+        --------------------------------------
+        links
+        --------------------------------------
+        microscope : Microscope
+        light_source : LightSource
+        optical_channel : MicroscopyOpticalChannel
+    }
+
+    class PlanarMicroscopySeries {
+        <<MicroscopySeries>>
+
+        --------------------------------------
+        datasets
+        --------------------------------------
+        data : (frame x height x width) numeric
+        --> unit : text
+        
+        --------------------------------------
+        links
+        --------------------------------------
+        imaging_space : PlanarImagingSpace
+    }
+
+    class VariableDepthMicroscopySeries {
+        <<MicroscopySeries>>
+
+        --------------------------------------
+        datasets
+        --------------------------------------
+        data : (frame x height x width) numeric
+        --> unit : text
+        depth_per_frame : (frame,) numeric
+        -- > unit : text, default="micrometers"
+        
+        --------------------------------------
+        links
+        --------------------------------------
+        imaging_space : PlanarImagingSpace
+    }
+
+    class VolumetricMicroscopySeries {
+        <<MicroscopySeries>>
+
+        --------------------------------------
+        datasets
+        --------------------------------------
+        data : (frame x height x width x depth) numeric
+        --> unit : text
+        
+        --------------------------------------
+        links
+        --------------------------------------
+        imaging_space : VolumetricImageSpace
+    }
+
+    class ImagingSpace{
+        <<NWBContainer>>
+
+        --------------------------------------
+        datasets
+        --------------------------------------
+        description : text
+        origin_coordinates : (x, y, z) numeric, optional
+        --> unit : text, default="micrometers"
+        
+        --------------------------------------
+        attributes
+        --------------------------------------
+        location : text, optional
+    }
+
+    class PlanarImagingSpace{
+        <<ImagingSpace>>
+
+        --------------------------------------
+        datasets
+        --------------------------------------
+        grid_spacing : (x, y) numeric, optional
+        --> unit : text, default="micrometers"
+        
+        --------------------------------------
+        attributes
+        --------------------------------------
+        reference_frame : text, optional
+    }
+
+    class VolumetricImagingSpace{
+        <<ImagingSpace>>
+
+        --------------------------------------
+        datasets
+        --------------------------------------
+        grid_spacing : (x, y, z) numeric, optional
+        --> unit : text, default="micrometers"
+        
+        --------------------------------------
+        attributes
+        --------------------------------------
+        reference_frame : text, optional
+    }
+
+    class MicroscopyOpticalChannel{
+        <<NWBContainer>>
+
+        --------------------------------------
+        datasets
+        --------------------------------------
+        description : text
+        
+        --------------------------------------
+        attributes
+        --------------------------------------
+        indicator : text
+        filter_description : text, optional
+        emission_wavelength_in_nm : numeric, optional
+    }
+
+    class LightSource{
+        <<Device>>
+
+        --------------------------------------
+        attributes
+        --------------------------------------
+        model : text, optional
+        filter_description : text, optional
+        excitation_wavelength_in_nm : numeric, optional
+        peak_power_in_W : numeric, optional
+        peak_pulse_energy_in_J : numeric, optional
+        intensity_in_W_per_m2 : numeric, optional
+        exposure_time_in_s : numeric, optional
+        pulse_rate_in_Hz : numeric, optional
+    }
+    
+    class Microscope{
+        <<Device>>
+        
+        --------------------------------------
+        attributes
+        --------------------------------------
+        model : text, optional
+    }
 
+    PlanarMicroscopySeries *-- MicroscopySeries : extends
+    PlanarMicroscopySeries -- PlanarImagingSpace : links
+    VariableDepthMicroscopySeries *-- MicroscopySeries : extends
+    VariableDepthMicroscopySeries -- PlanarImagingSpace : links
+    VolumetricMicroscopySeries *-- MicroscopySeries : extends
+    VolumetricMicroscopySeries -- VolumetricImageSpace : links
+    MicroscopySeries ..> Microscope : links
+    MicroscopySeries ..> LightSource : links
+    MicroscopySeries ..> MicroscopyOpticalChannel : links
 ```
 
 ---