Revise Allen notebook 6 - read only sbxreader memmap requirement

Author: CBroz1

notebooks/2022-allen-institute-workshop.ipynb

@@ -514,7 +514,7 @@
     "                  'h5py_key': 'data',\n",
     "                  'save_path0': [],\n",
     "                  'subfolders': [],\n",
-    "                  'nplanes': 1,\n",
+    "                  'nplanes': 4,\n",
     "                  'nchannels': 1,\n",
     "                  'functional_chan': 1,\n",
     "                  'tau': 1.0,\n",
@@ -630,9 +630,7 @@
    "id": "637b9ec1",
    "metadata": {},
    "source": [
-    "If you have write access to the data, you can then run Suite2p for the new parameter set and save the results to the respective tables.\n",
-    "\n",
-    "**Note:** CodeBook does not yet support write access for shared datasets. To see Suite2p triggering in action, contact [email protected] to find out how to upload your own data."
+    "You can then run Suite2p for the new parameter set and save the results to the respective tables. For this dataset (4 channels, 4 depths, 7.5k frames), this may take several hours."
    ]
   },
   {

notebooks/py_scripts/2022-allen-institute-workshop.py

@@ -237,7 +237,7 @@
                   'h5py_key': 'data',
                   'save_path0': [],
                   'subfolders': [],
-                  'nplanes': 1,
+                  'nplanes': 4,
                   'nchannels': 1,
                   'functional_chan': 1,
                   'tau': 1.0,
@@ -317,9 +317,7 @@
 
 imaging.ProcessingTask()
 
-# If you have write access to the data, you can then run Suite2p for the new parameter set and save the results to the respective tables.
-#
-# **Note:** CodeBook does not yet support write access for shared datasets. To see Suite2p triggering in action, contact [email protected] to find out how to upload your own data.
+# You can then run Suite2p for the new parameter set and save the results to the respective tables. For this dataset (4 channels, 4 depths, 7.5k frames), this may take several hours.
 
 # +
 populate_settings = dict(display_progress=True)

requirements.txt

@@ -7,6 +7,6 @@ element-event @ git+https://github.com/datajoint/element-event.git
 element-interface @ git+https://github.com/datajoint/element-interface.git
 ipykernel>=6.0.1
 jupytext>=1.13.7
-sbxreader
+sbxreader @ git+https://github.com/CBroz1/sbxreader
 nd2
 suite2p @ git+https://github.com/datajoint-company/suite2p.git