Make the flow of calcium imaging similar to that of ephys.

Author: shenshan

calcium_imaging/02-Imported Tables - Completed.ipynb

@@ -0,0 +1,62 @@
+import datajoint as dj
+import numpy as np
+import os
+from skimage import io
+
+# import the mouse-session schema
+from tutorial_pipeline.mouse_session import schema, Mouse, Session
+
+
+# Table definitions
+
+@schema
+class Scan(dj.Manual):
+    definition = """
+    -> Session
+    scan_idx    : int           # scan index
+    ---
+    depth       : float         # depth of this scan
+    wavelength  : float         # wavelength used
+    laser_power : float         # power of the laser used
+    fps         : float         # frames per second
+    file_name    : varchar(128) # name of the tif file
+    """
+
+
+@schema
+class AverageFrame(dj.Imported):
+    definition = """
+    -> Scan
+    ---
+    average_frame   : longblob     # average fluorescence across frames
+    """
+    def make(self, key):  # key is the primary key of one of the entries in the table `Scan`
+        # fetch data directory from table Session
+        data_path = (Session & key).fetch1('data_path')
+        
+        # fetch data file name from table Scan
+        file_name = (Scan & key).fetch1('file_name')
+        
+        # load the file
+        im = io.imread(os.path.join(data_path, file_name))
+        # compute the average image across the frames
+        avg_image = np.mean(im, axis=0)
+        
+        # Now prepare the entry as a dictionary with all fields defined in the table.
+        key['average_frame'] = avg_image # inherit the primary key from the table Scan
+        
+        # insert entry with the method `insert1()`
+        self.insert1(key)
+        
+        print('\tPopulated Scan {mouse_id} - {session_date} - {scan_idx}'.format(**key))
+
+Scan.insert([
+    {'mouse_id': 0, 'session_date': '2017-05-15', 'scan_idx': 1, 
+     'depth': 150, 'wavelength': 920, 'laser_power': 26, 'fps': 15, 'file_name': 'example_scan_01.tif'},
+    {'mouse_id': 0, 'session_date': '2017-05-15', 'scan_idx': 2, 
+     'depth': 200, 'wavelength': 920, 'laser_power': 24, 'fps': 15, 'file_name': 'example_scan_02.tif'},
+    {'mouse_id': 100, 'session_date': '2017-05-25', 'scan_idx': 1,
+     'depth': 150, 'wavelength': 920, 'laser_power': 25, 'fps': 15, 'file_name': 'example_scan_03.tif'}],
+    skip_duplicates=True)
+
+AverageFrame.populate()

calcium_imaging/02-Imported Tables - Interactive.ipynb

@@ -48,19 +48,27 @@ class Session(dj.Manual):
  {'experiment_setup': 0,
   'experimenter': 'Edgar Y. Walker',
   'mouse_id': 0,
-  'session_date': "2017-05-15"},
+  'session_date': "2017-05-15",
+  'data_path': 'data'
+ },
  {'experiment_setup': 0,
   'experimenter': 'Edgar Y. Walker',
   'mouse_id': 0,
-  'session_date': "2017-05-19"},
+  'session_date': "2017-05-19",
+  'data_path': 'data'
+ },
  {'experiment_setup': 1,
   'experimenter': 'Fabian Sinz',
   'mouse_id': 5,
-  'session_date': "2017-01-05"},
+  'session_date': "2017-01-05",
+  'data_path': 'data'
+ },
  {'experiment_setup': 100,
   'experimenter': 'Jacob Reimer',
   'mouse_id': 100,
-  'session_date': "2017-05-25"}
+  'session_date': "2017-05-25",
+  'data_path': 'data'
+ }
 ]
 
 Mouse.insert(mouse_data, skip_duplicates=True)