Skip to content

Commit b9a5b36

Browse files
alessandratrapanialessandratrapani
committed
update README
1 parent f83d089 commit b9a5b36

File tree

1 file changed

+42
-163
lines changed

1 file changed

+42
-163
lines changed

‎README.md‎

Lines changed: 42 additions & 163 deletions
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@ A Neurodata Without Borders (NWB) extension for storing microscopy data and asso
4343

4444
## Entity Relationship Diagrams
4545

46-
#### Device Components
46+
#### Experiment Metadata Components
4747

4848
```mermaid
4949
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
@@ -84,6 +84,17 @@ classDiagram
8484
technique : text, optional
8585
}
8686
87+
class MicroscopyExperimentMetadata {
88+
<<LabMetaData>>
89+
--------------------------------------
90+
groups
91+
--------------------------------------
92+
**microscopy_rigs** : MicroscopyRig[0..*]
93+
**viral_vectors** : ViralVector[0..*]
94+
**viral_vector_injections** : ViralVectorInjection[0..*]
95+
**indicators** : Indicator[0..*]
96+
}
97+
8798
class MicroscopyRig {
8899
<<NWBContainer>>
89100
--------------------------------------
@@ -105,80 +116,35 @@ classDiagram
105116
optical_path_scheme : Image, optional
106117
}
107118
108-
class ExcitationSource {
109-
<<Device>>
110-
--------------------------------------
111-
attributes
112-
--------------------------------------
113-
**illumination_type** : text
114-
**excitation_wavelength_in_nm** : float
115-
**excitation_mode** : text
116-
power_in_W : float, optional
117-
intensity_in_W_per_m2 : float, optional
118-
exposure_time_in_s : float, optional
119-
}
120-
121-
class PulsedExcitationSource {
122-
<<ExcitationSource>>
123-
--------------------------------------
124-
attributes
125-
--------------------------------------
126-
peak_power_in_W : float, optional
127-
peak_pulse_energy_in_J : float, optional
128-
pulse_rate_in_Hz : float, optional
129-
}
130-
131-
class OpticalFilter {
132-
<<Device>>
133-
--------------------------------------
134-
attributes
135-
--------------------------------------
136-
**filter_type** : text
137-
}
138-
139-
class BandOpticalFilter {
140-
<<OpticalFilter>>
141-
--------------------------------------
142-
attributes
143-
--------------------------------------
144-
**center_wavelength_in_nm** : float
145-
**bandwidth_in_nm** : float
146-
}
147-
148-
class EdgeOpticalFilter {
149-
<<OpticalFilter>>
150-
--------------------------------------
151-
attributes
152-
--------------------------------------
153-
**cut_wavelength_in_nm** : float
154-
slope_in_percent_cut_wavelength : float, optional
155-
slope_starting_transmission_in_percent : float, optional
156-
slope_ending_transmission_in_percent : float, optional
157-
}
158-
159-
class DichroicMirror {
160-
<<Device>>
119+
class ViralVector {
120+
<<NWBContainer>>
161121
--------------------------------------
162122
attributes
163123
--------------------------------------
164-
cut_on_wavelength_in_nm : numeric, optional
165-
cut_off_wavelength_in_nm : numeric, optional
166-
reflection_band_in_nm : numeric, optional
167-
transmission_band_in_nm : numeric, optional
168-
angle_of_incidence_in_degrees : numeric, optional
124+
**construct_name** : text
125+
titer_in_vg_per_ml : numeric, optional
126+
manufacturer : text, optional
127+
description : text, optional
169128
}
170-
171-
class Photodetector {
172-
<<Device>>
129+
class ViralVectorInjection {
130+
<<NWBContainer>>
173131
--------------------------------------
174132
attributes
175133
--------------------------------------
176-
**detector_type** : text
177-
**detected_wavelength_in_nm** : float
178-
gain : float, optional
179-
gain_unit : text, optional
180-
}
181-
134+
location : text, optional
135+
hemisphere : text, optional
136+
ap_in_mm : numeric, optional
137+
ml_in_mm : numeric, optional
138+
dv_in_mm : numeric, optional
139+
pitch_in_deg : numeric, optional
140+
yaw_in_deg : numeric, optional
141+
roll_in_deg : numeric, optional
142+
stereotactic_rotation_in_deg : numeric, optional
143+
stereotactic_tilt_in_deg : numeric, optional
144+
volume_in_uL : numeric, optional
145+
injection_date : text, optional
146+
**viral_vector** : ViralVector
147+
}
182148
class Indicator {
183149
<<NWBContainer>>
184150
--------------------------------------
@@ -187,19 +153,20 @@ classDiagram
187153
**label** : text
188154
description : text, optional
189155
manufacturer : text, optional
190-
injection_brain_region : text, optional
191-
injection_coordinates_in_mm : float[3], optional
156+
**viral_vector_injection** : ViralVectorInjection, optional
192157
}
193158
159+
194160
DeviceModel <|-- MicroscopeModel : extends
195161
Device <|-- Microscope : extends
196-
197162
Microscope o--> MicroscopeModel : links
198163
MicroscopyRig o--> Microscope : links
199-
MicroscopyRig o--> ExcitationSource : links
200-
MicroscopyRig o--> OpticalFilter : links
201-
MicroscopyRig o--> DichroicMirror : links
202-
MicroscopyRig o--> Photodetector : links
164+
MicroscopyExperimentMetadata *-- MicroscopyRig : contains
165+
MicroscopyExperimentMetadata *-- ViralVector : contains
166+
MicroscopyExperimentMetadata *-- ViralVectorInjection : contains
167+
MicroscopyExperimentMetadata *-- Indicator : contains
168+
ViralVectorInjection o--> ViralVector : links
169+
Indicator o--> ViralVectorInjection : links
203170
```
204171

205172
#### Illumination Pattern Components
@@ -267,94 +234,6 @@ classDiagram
267234
ImagingSpace *-- IlluminationPattern : contains
268235
```
269236

270-
#### Experiment Metadata Components
271-
272-
```mermaid
273-
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
274-
275-
classDiagram
276-
direction TB
277-
278-
class MicroscopyExperimentMetadata {
279-
<<LabMetaData>>
280-
--------------------------------------
281-
groups
282-
--------------------------------------
283-
**microscopy_rigs** : MicroscopyRig[0..*]
284-
**viral_vectors** : ViralVector[0..*]
285-
**viral_vector_injections** : ViralVectorInjection[0..*]
286-
**indicators** : Indicator[0..*]
287-
}
288-
289-
class MicroscopyRig {
290-
<<NWBContainer>>
291-
--------------------------------------
292-
attributes
293-
--------------------------------------
294-
description : text
295-
--------------------------------------
296-
links
297-
--------------------------------------
298-
microscope : Microscope
299-
excitation_source : ExcitationSource, optional
300-
excitation_filter : OpticalFilter, optional
301-
dichroic_mirror : DichroicMirror, optional
302-
photodetector : Photodetector, optional
303-
emission_filter : OpticalFilter, optional
304-
--------------------------------------
305-
groups
306-
--------------------------------------
307-
optical_path_scheme : Image, optional
308-
}
309-
310-
class ViralVector {
311-
<<NWBContainer>>
312-
--------------------------------------
313-
attributes
314-
--------------------------------------
315-
**construct_name** : text
316-
titer_in_vg_per_ml : numeric, optional
317-
manufacturer : text, optional
318-
description : text, optional
319-
}
320-
class ViralVectorInjection {
321-
<<NWBContainer>>
322-
--------------------------------------
323-
attributes
324-
--------------------------------------
325-
location : text, optional
326-
hemisphere : text, optional
327-
ap_in_mm : numeric, optional
328-
ml_in_mm : numeric, optional
329-
dv_in_mm : numeric, optional
330-
pitch_in_deg : numeric, optional
331-
yaw_in_deg : numeric, optional
332-
roll_in_deg : numeric, optional
333-
stereotactic_rotation_in_deg : numeric, optional
334-
stereotactic_tilt_in_deg : numeric, optional
335-
volume_in_uL : numeric, optional
336-
injection_date : text, optional
337-
**viral_vector** : ViralVector
338-
}
339-
class Indicator {
340-
<<NWBContainer>>
341-
--------------------------------------
342-
attributes
343-
--------------------------------------
344-
**label** : text
345-
description : text, optional
346-
manufacturer : text, optional
347-
**viral_vector_injection** : ViralVectorInjection, optional
348-
}
349-
350-
MicroscopyExperimentMetadata *-- MicroscopyRig : contains
351-
MicroscopyExperimentMetadata *-- ViralVector : contains
352-
MicroscopyExperimentMetadata *-- ViralVectorInjection : contains
353-
MicroscopyExperimentMetadata *-- Indicator : contains
354-
ViralVectorInjection o--> ViralVector : links
355-
Indicator o--> ViralVectorInjection : links
356-
```
357-
358237
#### Microscopy Series and Imaging Space Components
359238

360239
```mermaid

0 commit comments

Comments
 (0)