atlab · dimitri-yatsenko · Jun 27, 2016 · May 16, 2016 · Jun 14, 2016 · Jun 14, 2016
diff --git a/python/commons/bs.py b/python/commons/bs.py
@@ -2,3 +2,4 @@
 
 schema = dj.schema('dimitri_brain_state', locals())
 
+schema.spawn_missing_classes()
diff --git a/python/commons/common.py b/python/commons/common.py
@@ -3,3 +3,4 @@
 schema = dj.schema('common', locals())
 
 
+schema.spawn_missing_classes()
diff --git a/python/commons/inj.py b/python/commons/inj.py
@@ -0,0 +1,81 @@
+import datajoint as dj
+from commons import virus, mice
+
+schema = dj.schema('common_injections', locals())
+
+
+@schema
+class Site(dj.Lookup):
+    definition = """
+    # Injection target site
+
+    injection_site               : char(8) # ID
+    ---
+    """
+
+    @property
+    def contents(self):
+        yield from zip(['V1', 'dLGN', 'AL', 'LM', 'S1','S2','M1', 'PM'])
+
+
+@schema
+class AtlasStereotacticTargets(dj.Lookup):
+    definition = """
+    # Unadjusted stereotactic coordinates from the mouse brain atlas
+
+    ->Site
+    target_id                     : char(20) # ID for this set of coordinates
+    ---
+    caudal                        : double # coordinate caudal from bregma in mm
+    lateral                       : double # lateral coordinate in mm
+    ventral                       : double # coordinate ventral from cortical surface in mm
+    lambda_bregma_basedist=4.21   : double # base distance between lambda and bregma from the stereotactic atlas in mm
+    """
+    contents = [
+        dict(injection_site='dLGN', target_id='Tang2016', caudal=2.6, lateral=2.15, ventral=2.7),
+        dict(injection_site='V1',   target_id='fabee01',  caudal=3.8, lateral=2.5,  ventral=0.3),
+    ]
+
+@schema
+class GuidanceMethod(dj.Lookup):
+    definition = """
+    # guidance method for injections
+
+    guidance                    : char(20)
+    ---
+    """
+
+    @property
+    def contents(self):
+        yield from zip(['2P','stereotactic','intrinsic','other'])
+
+@schema
+class VirusInjection(dj.Manual):
+    definition = """
+    # Virus Injection
+
+    -> mice.Mice
+    -> virus.Virus
+    -> Site
+    ---
+    -> GuidanceMethod
+    volume=null                   : double      # injection volume in nl
+    speed=null                    : double      # injection speed [nl/min]
+    toi=CURRENT_TIMESTAMP         : timestamp   # time of injection
+    """
+
+@schema
+class InjectionLocation(dj.Manual):
+    definition = """
+    # Adjusted stereotactic coordinates for injection
+
+    ->VirusInjection
+    ->AtlasStereotacticTargets
+    ---
+    lambda_bregma                 : double    # distance between lambda and bregma in mm as measured
+    caudal                        : double    # coordinate caudal from bregma in mm
+    lateral                       : double    # lateral coordinate in mm
+    ventral                       : double    # coordinate ventral from cortical surface in mm
+    adjustment                    : double    # adjustement factor to convert atlas coordinates to this injection
+    toi=CURRENT_TIMESTAMP         : timestamp # time of injection
+    """
diff --git a/python/commons/mc.py b/python/commons/mc.py
@@ -2,3 +2,4 @@
 
 schema = dj.schema('common_microcolumns', locals())
 
+schema.spawn_missing_classes()
diff --git a/python/commons/mice.py b/python/commons/mice.py
@@ -2,3 +2,4 @@
 
 schema = dj.schema('common_mice', locals())
 
+schema.spawn_missing_classes()
diff --git a/python/commons/mp.py b/python/commons/mp.py
@@ -2,3 +2,4 @@
 
 schema = dj.schema('common_multipatch', locals())
 
+schema.spawn_missing_classes()
diff --git a/python/commons/opt.py b/python/commons/opt.py
@@ -2,3 +2,4 @@
 
 schema = dj.schema('common_optical', locals())
 
+schema.spawn_missing_classes()
diff --git a/python/commons/psy.py b/python/commons/psy.py
@@ -2,3 +2,4 @@
 
 schema = dj.schema('common_psy', locals())
 
+schema.spawn_missing_classes()
diff --git a/python/commons/pupil.py b/python/commons/pupil.py
@@ -3,3 +3,4 @@
 schema = dj.schema('dimitri_pupil', locals())
 
 
+schema.spawn_missing_classes()
diff --git a/python/commons/reso.py b/python/commons/reso.py
@@ -1,3 +1,4 @@
 import datajoint as dj
 
 schema = dj.schema('common_resonant', locals())
+schema.spawn_missing_classes()
diff --git a/python/commons/tp.py b/python/commons/tp.py
@@ -3,3 +3,4 @@
 schema = dj.schema('common_two_photon', locals())
 
 
+schema.spawn_missing_classes()
diff --git a/python/commons/virus.py b/python/commons/virus.py
@@ -3,8 +3,6 @@
 schema = dj.schema('common_virus', locals())
 
 
-
-
 @schema
 class Gene(dj.Manual):
     definition = """
@@ -17,13 +15,16 @@ class Gene(dj.Manual):
     risk="no known risk"        : varchar(512) # risk for humans
     """
 
+
 @schema
 class Construct(dj.Manual):
     definition = """
     # combinations of several genes
 
     construct_id        : char(80)
     """
+
+
 @schema
 class ConstructGene(dj.Manual):
     definition = """
@@ -33,6 +34,7 @@ class ConstructGene(dj.Manual):
     gene_name       : char(30) # name of the gene
     """
 
+
 @schema
 class Type(dj.Lookup):
     definition = """
@@ -43,7 +45,7 @@ class Type(dj.Lookup):
 
     """
 
-    contents = [(t,) for t in ['AAV', 'Rabies', 'Lenti','Herpes']]
+    contents = [(t,) for t in ['AAV', 'Rabies', 'Lenti', 'Herpes']]
 
 
 @schema
@@ -57,7 +59,7 @@ class Source(dj.Lookup):
 
     @property
     def contents(self):
-        yield from zip(['Penn', 'UNC', 'Homegrown', 'MIT'])
+        yield from zip(['Penn', 'UNC', 'Homegrown',  'MIT', 'AToliasLab'])
 
 
 @schema

diff --git a/schemas/+inj/AtlasStereotacticTargets.m b/schemas/+inj/AtlasStereotacticTargets.m
@@ -0,0 +1,14 @@
+%{
+inj.AtlasStereotacticTargets (lookup) # Unadjusted stereotactic coordinates from the mouse brain atlas
+->inj.Site
+target_id                     : char(20) # ID for this set of coordinates
+---
+caudal                        : double # coordinate caudal from bregma in mm
+lateral                       : double # lateral coordinate in mm
+ventral                       : double # coordinate ventral from cortical surface in mm
+lambda_bregma_basedist=4.21   : double # base distance between lambda and bregma from the stereotactic atlas in mm
+%}
+
+
+classdef AtlasStereotacticTargets < dj.Relvar
+end
diff --git a/schemas/+inj/GuidanceMethod.m b/schemas/+inj/GuidanceMethod.m
@@ -0,0 +1,10 @@
+%{
+inj.GuidanceMethod (lookup) # guidance method for injections
+
+guidance        : char(20)
+---
+%}
+
+
+classdef GuidanceMethod < dj.Relvar
+end
diff --git a/schemas/+inj/InjectionLocation.m b/schemas/+inj/InjectionLocation.m
@@ -0,0 +1,17 @@
+%{
+inj.InjectionLocation (manual) # Adjusted stereotactic coordinates for injection
+
+->inj.VirusInjection
+->inj.AtlasStereotacticTargets
+---
+lambda_bregma                 : double    # distance between lambda and bregma in mm as measured
+caudal                        : double    # coordinate caudal from bregma in mm
+lateral                       : double    # lateral coordinate in mm
+ventral                       : double    # coordinate ventral from cortical surface in mm
+adjustment                    : double    # adjustement factor to convert atlas coordinates to this injection
+toi=CURRENT_TIMESTAMP         : timestamp # time of injection
+%}
+
+
+classdef InjectionLocation < dj.Relvar
+end
diff --git a/schemas/+inj/Site.m b/schemas/+inj/Site.m
@@ -0,0 +1,9 @@
+%{
+inj.Site (lookup) # Injection target site
+injection_site               : char(8) # ID
+---
+%}
+
+
+classdef Site < dj.Relvar
+end
diff --git a/schemas/+inj/VirusInjection.m b/schemas/+inj/VirusInjection.m
@@ -0,0 +1,16 @@
+%{
+inj.VirusInjection (manual) # Virus Injection
+
+-> mice.Mice
+-> virus.Virus
+-> inj.Site
+---
+-> inj.GuidanceMethod
+volume=null                   : double      # injection volume in nl
+speed=null                    : double      # injection speed [nl/min]
+toi=CURRENT_TIMESTAMP         : timestamp   # time of injection
+%}
+
+
+classdef VirusInjection < dj.Relvar
+end
diff --git a/schemas/+inj/getSchema.m b/schemas/+inj/getSchema.m
@@ -0,0 +1,7 @@
+function obj = getSchema
+persistent schemaObject
+if isempty(schemaObject)
+    schemaObject = dj.Schema(dj.conn, 'inj', 'common_injections');
+end
+obj = schemaObject;
+end
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,3 +2,4 @@

		schema = dj.schema('dimitri_brain_state', locals())

		schema.spawn_missing_classes()
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Expand Up		@@ -3,3 +3,4 @@
		schema = dj.schema('common', locals())


		schema.spawn_missing_classes()
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Expand Up		@@ -2,3 +2,4 @@

		schema = dj.schema('common_microcolumns', locals())

		schema.spawn_missing_classes()
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Expand Up		@@ -2,3 +2,4 @@

		schema = dj.schema('common_mice', locals())

		schema.spawn_missing_classes()
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Expand Up		@@ -2,3 +2,4 @@

		schema = dj.schema('common_multipatch', locals())

		schema.spawn_missing_classes()
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Expand Up		@@ -2,3 +2,4 @@

		schema = dj.schema('common_optical', locals())

		schema.spawn_missing_classes()
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Expand Up		@@ -2,3 +2,4 @@

		schema = dj.schema('common_psy', locals())

		schema.spawn_missing_classes()
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Expand Up		@@ -3,3 +3,4 @@
		schema = dj.schema('dimitri_pupil', locals())


		schema.spawn_missing_classes()
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Expand Up		@@ -3,3 +3,4 @@
		schema = dj.schema('common_two_photon', locals())


		schema.spawn_missing_classes()