From 8a9f06d0e986f22d86a9cc3042d35320319408e5 Mon Sep 17 00:00:00 2001
From: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
Date: Tue, 7 Nov 2023 21:59:50 +0000
Subject: [PATCH 1/2] Install `elements` in DevContainer

---
 .devcontainer/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index f8b4297..7cb9a7b 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -33,7 +33,7 @@ RUN \
     # pipeline dependencies
     apt-get install gcc g++ ffmpeg libsm6 libxext6 -y && \
     pip install numpy Cython && \
-    pip install --no-cache-dir -e /tmp/element-miniscope[caiman_requirements,caiman] && \
+    pip install --no-cache-dir -e /tmp/element-miniscope[elements,caiman_requirements,caiman] && \
     caimanmanager.py install && \
     # clean up
     rm -rf /tmp/element-miniscope && \

From e203726195f51407b8b851343322d3be1adb2088 Mon Sep 17 00:00:00 2001
From: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
Date: Wed, 8 Nov 2023 21:51:13 +0000
Subject: [PATCH 2/2] Revert paramset_idx to paramset_id

---
 element_miniscope/miniscope.py |   14 +-
 notebooks/tutorial.ipynb       | 1740 +++++++++++++++++++++++++++++---
 2 files changed, 1633 insertions(+), 121 deletions(-)

diff --git a/element_miniscope/miniscope.py b/element_miniscope/miniscope.py
index d5c34ba..6faeed0 100644
--- a/element_miniscope/miniscope.py
+++ b/element_miniscope/miniscope.py
@@ -366,7 +366,7 @@ class ProcessingParamSet(dj.Lookup):
     """Parameters of the processing method.
 
     Attributes:
-        paramset_idx (foreign key, smallint): Unique parameter set ID.
+        paramset_id (foreign key, smallint): Unique parameter set ID.
         ProcessingMethod (varchar(16) ): ProcessingMethod from the lookup table.
         paramset_desc (varchar(128) ): Description of the parameter set.
         paramset_set_hash (uuid): UUID hash for parameter set.
@@ -375,7 +375,7 @@ class ProcessingParamSet(dj.Lookup):
 
     definition = """
     # Parameter set used for processing of miniscope data
-    paramset_idx:  smallint
+    paramset_id:  smallint
     ---
     -> ProcessingMethod
     paramset_desc: varchar(128)
@@ -388,7 +388,7 @@ class ProcessingParamSet(dj.Lookup):
     def insert_new_params(
         cls,
         processing_method: str,
-        paramset_idx: int,
+        paramset_id: int,
         paramset_desc: str,
         params: dict,
         processing_method_desc: str = "",
@@ -397,7 +397,7 @@ def insert_new_params(
 
         Args:
             processing_method (str): Name of the processing method or software.
-            paramset_idx (int): Unique number for the set of processing parameters.
+            paramset_id (int): Unique number for the set of processing parameters.
             paramset_desc (str): Description of the processing parameter set.
             params (dict): Dictionary of processing parameters for the selected processing_method.
             processing_method_desc (str, optional): Description of the processing method. Defaults to "".
@@ -411,7 +411,7 @@ def insert_new_params(
         )
         param_dict = {
             "processing_method": processing_method,
-            "paramset_idx": paramset_idx,
+            "paramset_id": paramset_id,
             "paramset_desc": paramset_desc,
             "params": params,
             "param_set_hash": dict_to_uuid(params),
@@ -419,8 +419,8 @@ def insert_new_params(
         q_param = cls & {"param_set_hash": param_dict["param_set_hash"]}
 
         if q_param:  # If the specified param-set already exists
-            pname = q_param.fetch1("paramset_idx")
-            if pname == paramset_idx:  # If the existed set has the same name: job done
+            pname = q_param.fetch1("paramset_id")
+            if pname == paramset_id:  # If the existed set has the same name: job done
                 return
             else:  # If not same name: human error, try adding with different name
                 raise dj.DataJointError(
diff --git a/notebooks/tutorial.ipynb b/notebooks/tutorial.ipynb
index c3abb08..66c0448 100644
--- a/notebooks/tutorial.ipynb
+++ b/notebooks/tutorial.ipynb
@@ -8,9 +8,9 @@
     "# DataJoint Elements Tutorial: Miniscope\n",
     "\n",
     "Welcome to the tutorial for DataJoint's open-source data pipeline for miniature\n",
-    "fluorescent microscopes (miniscope). This tutorial aims to provide a comprehensive understanding of the\n",
+    "fluorescent microscope imaging (miniscope). This tutorial aims to provide a comprehensive understanding of the\n",
     "open-source data pipeline created using `element-miniscope` for processing\n",
-    "and analyzing calcium dynamics in neurons. \n",
+    "and analyzing neuronal calcium dynamics acquired with the UCLA Miniscope and Miniscope DAQ. \n",
     "\n",
     "**In this tutorial, we will cover:**\n",
     "- The basics:\n",
@@ -35,7 +35,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -83,9 +83,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "[2023-11-08 21:19:10,053][WARNING]: lab.Project and related tables will be removed in a future version of Element Lab. Please use the project schema.\n",
+      "[2023-11-08 21:19:10,055][INFO]: Connecting root@fakeservices.datajoint.io:3306\n",
+      "[2023-11-08 21:19:10,063][INFO]: Connected root@fakeservices.datajoint.io:3306\n"
+     ]
+    }
+   ],
    "source": [
     "from tutorial_pipeline import (\n",
     "    lab,\n",
@@ -104,9 +114,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Schema `neuro_subject`"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "subject.schema"
    ]
@@ -120,9 +141,101 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "    \n",
+       "    <style type=\"text/css\">\n",
+       "        .Table{\n",
+       "            border-collapse:collapse;\n",
+       "        }\n",
+       "        .Table th{\n",
+       "            background: #A0A0A0; color: #ffffff; padding:4px; border:#f0e0e0 1px solid;\n",
+       "            font-weight: normal; font-family: monospace; font-size: 100%;\n",
+       "        }\n",
+       "        .Table td{\n",
+       "            padding:4px; border:#f0e0e0 1px solid; font-size:100%;\n",
+       "        }\n",
+       "        .Table tr:nth-child(odd){\n",
+       "            background: #ffffff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        .Table tr:nth-child(even){\n",
+       "            background: #f3f1ff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        /* Tooltip container */\n",
+       "        .djtooltip {\n",
+       "        }\n",
+       "        /* Tooltip text */\n",
+       "        .djtooltip .djtooltiptext {\n",
+       "            visibility: hidden;\n",
+       "            width: 120px;\n",
+       "            background-color: black;\n",
+       "            color: #fff;\n",
+       "            text-align: center;\n",
+       "            padding: 5px 0;\n",
+       "            border-radius: 6px;\n",
+       "            /* Position the tooltip text - see examples below! */\n",
+       "            position: absolute;\n",
+       "            z-index: 1;\n",
+       "        }\n",
+       "        #primary {\n",
+       "            font-weight: bold;\n",
+       "            color: black;\n",
+       "        }\n",
+       "        #nonprimary {\n",
+       "            font-weight: normal;\n",
+       "            color: white;\n",
+       "        }\n",
+       "\n",
+       "        /* Show the tooltip text when you mouse over the tooltip container */\n",
+       "        .djtooltip:hover .djtooltiptext {\n",
+       "            visibility: visible;\n",
+       "        }\n",
+       "    </style>\n",
+       "    \n",
+       "    <b></b>\n",
+       "        <div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
+       "        <table border=\"1\" class=\"Table\">\n",
+       "            <thead> <tr style=\"text-align: right;\"> <th> <div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">subject</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">subject_nickname</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">sex</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">subject_birth_date</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">subject_description</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div> </th> </tr> </thead>\n",
+       "            <tbody> <tr>  </tr> </tbody>\n",
+       "        </table>\n",
+       "        \n",
+       "        <p>Total: 0</p></div>\n",
+       "        "
+      ],
+      "text/plain": [
+       "*subject    subject_nickna sex     subject_birth_ subject_descri\n",
+       "+---------+ +------------+ +-----+ +------------+ +------------+\n",
+       "\n",
+       " (Total: 0)"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "subject.Subject()"
    ]
@@ -138,9 +251,520 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "image/svg+xml": [
+       "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" width=\"1580pt\" height=\"719pt\" viewBox=\"0.00 0.00 1580.00 719.00\">\n",
+       "<g id=\"graph0\" class=\"graph\" transform=\"scale(1 1) rotate(0) translate(4 715)\">\n",
+       "<title>%3</title>\n",
+       "<polygon fill=\"white\" stroke=\"transparent\" points=\"-4,4 -4,-715 1576,-715 1576,4 -4,4\"/>\n",
+       "<!-- 0 -->\n",
+       "<g id=\"node1\" class=\"node\">\n",
+       "<title>0</title>\n",
+       "<ellipse fill=\"#ff8800\" fill-opacity=\"0.501961\" stroke=\"#ff8800\" stroke-opacity=\"0.501961\" cx=\"836.5\" cy=\"-205.5\" rx=\"2\" ry=\"2\"/>\n",
+       "<text text-anchor=\"middle\" x=\"836.5\" y=\"-205.2\" font-family=\"arial\" font-size=\"1.00\" fill=\"#ff8800\" fill-opacity=\"0.501961\">0</text>\n",
+       "</g>\n",
+       "<!-- miniscope.Fluorescence.Trace -->\n",
+       "<g id=\"node4\" class=\"node\">\n",
+       "<title>miniscope.Fluorescence.Trace</title>\n",
+       "<g id=\"a_node4\"><a xlink:title=\"→ miniscope.Fluorescence\r→ miniscope.Segmentation.Mask\r→ miniscope.Channel.proj(fluorescence_channel=&quot;channel&quot;)\r------------------------------\rfluorescence         \rneuropil_fluorescence=null \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"1013.5,-77.5 863.5,-77.5 863.5,-58.5 1013.5,-58.5 1013.5,-77.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"938.5\" y=\"-65.5\" font-family=\"arial\" font-size=\"10.00\">miniscope.Fluorescence.Trace</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- 0&#45;&gt;miniscope.Fluorescence.Trace -->\n",
+       "<g id=\"edge1\" class=\"edge\">\n",
+       "<title>0-&gt;miniscope.Fluorescence.Trace</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M836.41,-203.11C835.91,-194.33 834.25,-146.14 855.5,-117 869.53,-97.77 893.78,-85.04 912.46,-77.56\"/>\n",
+       "</g>\n",
+       "<!-- 1 -->\n",
+       "<g id=\"node2\" class=\"node\">\n",
+       "<title>1</title>\n",
+       "<ellipse fill=\"#ff8800\" fill-opacity=\"0.501961\" stroke=\"#ff8800\" stroke-opacity=\"0.501961\" cx=\"895.5\" cy=\"-205.5\" rx=\"2\" ry=\"2\"/>\n",
+       "<text text-anchor=\"middle\" x=\"895.5\" y=\"-205.2\" font-family=\"arial\" font-size=\"1.00\" fill=\"#ff8800\" fill-opacity=\"0.501961\">1</text>\n",
+       "</g>\n",
+       "<!-- miniscope.Segmentation.Mask -->\n",
+       "<g id=\"node33\" class=\"node\">\n",
+       "<title>miniscope.Segmentation.Mask</title>\n",
+       "<g id=\"a_node33\"><a xlink:title=\"→ miniscope.Segmentation\rmask                 \r------------------------------\r→ miniscope.Channel.proj(segmentation_channel=&quot;channel&quot;)\rmask_npix            \rmask_center_x=null   \rmask_center_y=null   \rmask_xpix=null       \rmask_ypix=null       \rmask_weights         \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"1181,-144 1030,-144 1030,-125 1181,-125 1181,-144\"/>\n",
+       "<text text-anchor=\"start\" x=\"1038\" y=\"-133\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.Segmentation.Mask</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- 1&#45;&gt;miniscope.Segmentation.Mask -->\n",
+       "<g id=\"edge2\" class=\"edge\">\n",
+       "<title>1-&gt;miniscope.Segmentation.Mask</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-dasharray=\"5,2\" stroke-opacity=\"0.250980\" d=\"M897.32,-203.9C913.07,-198.73 1027.3,-161.2 1079.54,-144.03\"/>\n",
+       "</g>\n",
+       "<!-- 2 -->\n",
+       "<g id=\"node3\" class=\"node\">\n",
+       "<title>2</title>\n",
+       "<ellipse fill=\"#ff8800\" fill-opacity=\"0.501961\" stroke=\"#ff8800\" stroke-opacity=\"0.501961\" cx=\"561.5\" cy=\"-205.5\" rx=\"2\" ry=\"2\"/>\n",
+       "<text text-anchor=\"middle\" x=\"561.5\" y=\"-205.2\" font-family=\"arial\" font-size=\"1.00\" fill=\"#ff8800\" fill-opacity=\"0.501961\">2</text>\n",
+       "</g>\n",
+       "<!-- miniscope.MotionCorrection -->\n",
+       "<g id=\"node17\" class=\"node\">\n",
+       "<title>miniscope.MotionCorrection</title>\n",
+       "<g id=\"a_node17\"><a xlink:title=\"→ miniscope.Curation\r------------------------------\r→ miniscope.Channel.proj(motion_correct_channel=&quot;channel&quot;)\r\">\n",
+       "<ellipse fill=\"#00007f\" fill-opacity=\"0.250980\" stroke=\"#00007f\" stroke-opacity=\"0.250980\" cx=\"320.5\" cy=\"-134.5\" rx=\"104\" ry=\"17.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"320.5\" y=\"-131.4\" font-family=\"arial\" font-size=\"12.00\" fill=\"#00007f\" fill-opacity=\"0.627451\">miniscope.MotionCorrection</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- 2&#45;&gt;miniscope.MotionCorrection -->\n",
+       "<g id=\"edge3\" class=\"edge\">\n",
+       "<title>2-&gt;miniscope.MotionCorrection</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-dasharray=\"5,2\" stroke-opacity=\"0.250980\" d=\"M559.96,-204.06C545.77,-200 436.73,-168.78 370.78,-149.9\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.ProcessingQualityMetrics.Trace -->\n",
+       "<g id=\"node10\" class=\"node\">\n",
+       "<title>miniscope.ProcessingQualityMetrics.Trace</title>\n",
+       "<g id=\"a_node10\"><a xlink:title=\"→ miniscope.ProcessingQualityMetrics\r→ miniscope.Fluorescence.Trace\r------------------------------\rskewness             \rvariance             \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"1238,-19 1035,-19 1035,0 1238,0 1238,-19\"/>\n",
+       "<text text-anchor=\"middle\" x=\"1136.5\" y=\"-7\" font-family=\"arial\" font-size=\"10.00\">miniscope.ProcessingQualityMetrics.Trace</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Fluorescence.Trace&#45;&gt;miniscope.ProcessingQualityMetrics.Trace -->\n",
+       "<g id=\"edge4\" class=\"edge\">\n",
+       "<title>miniscope.Fluorescence.Trace-&gt;miniscope.ProcessingQualityMetrics.Trace</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M968.57,-58.42C1005.9,-47.77 1069.17,-29.71 1106.47,-19.07\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Activity.Trace -->\n",
+       "<g id=\"node16\" class=\"node\">\n",
+       "<title>miniscope.Activity.Trace</title>\n",
+       "<g id=\"a_node16\"><a xlink:title=\"→ miniscope.Activity\r→ miniscope.Fluorescence.Trace\r------------------------------\ractivity_trace       \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"850.5,-19 726.5,-19 726.5,0 850.5,0 850.5,-19\"/>\n",
+       "<text text-anchor=\"middle\" x=\"788.5\" y=\"-7\" font-family=\"arial\" font-size=\"10.00\">miniscope.Activity.Trace</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Fluorescence.Trace&#45;&gt;miniscope.Activity.Trace -->\n",
+       "<g id=\"edge5\" class=\"edge\">\n",
+       "<title>miniscope.Fluorescence.Trace-&gt;miniscope.Activity.Trace</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M915.72,-58.42C887.52,-47.8 839.79,-29.82 811.5,-19.16\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Fluorescence -->\n",
+       "<g id=\"node5\" class=\"node\">\n",
+       "<title>miniscope.Fluorescence</title>\n",
+       "<g id=\"a_node5\"><a xlink:title=\"→ miniscope.Segmentation\r\">\n",
+       "<ellipse fill=\"#ff0000\" fill-opacity=\"0.125490\" stroke=\"#ff0000\" stroke-opacity=\"0.125490\" cx=\"938.5\" cy=\"-134.5\" rx=\"13\" ry=\"13\"/>\n",
+       "<text text-anchor=\"middle\" x=\"938.5\" y=\"-131.4\" font-family=\"arial\" font-size=\"12.00\" fill=\"#7f0000\" fill-opacity=\"0.627451\">miniscope.Fluorescence</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Fluorescence&#45;&gt;miniscope.Fluorescence.Trace -->\n",
+       "<g id=\"edge6\" class=\"edge\">\n",
+       "<title>miniscope.Fluorescence-&gt;miniscope.Fluorescence.Trace</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M938.5,-121.37C938.5,-108.67 938.5,-89.04 938.5,-77.77\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Activity -->\n",
+       "<g id=\"node14\" class=\"node\">\n",
+       "<title>miniscope.Activity</title>\n",
+       "<g id=\"a_node14\"><a xlink:title=\"→ miniscope.Fluorescence\r→ miniscope.ActivityExtractionMethod\r\">\n",
+       "<ellipse fill=\"#ff0000\" fill-opacity=\"0.125490\" stroke=\"#ff0000\" stroke-opacity=\"0.125490\" cx=\"788.5\" cy=\"-68\" rx=\"13\" ry=\"13\"/>\n",
+       "<text text-anchor=\"middle\" x=\"788.5\" y=\"-64.9\" font-family=\"arial\" font-size=\"12.00\" fill=\"#7f0000\" fill-opacity=\"0.627451\">miniscope.Activity</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Fluorescence&#45;&gt;miniscope.Activity -->\n",
+       "<g id=\"edge7\" class=\"edge\">\n",
+       "<title>miniscope.Fluorescence-&gt;miniscope.Activity</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M926.73,-128.44C898.69,-116.38 828.2,-86.07 800.22,-74.04\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.ProcessingQualityMetrics -->\n",
+       "<g id=\"node28\" class=\"node\">\n",
+       "<title>miniscope.ProcessingQualityMetrics</title>\n",
+       "<g id=\"a_node28\"><a xlink:title=\"→ miniscope.Fluorescence\r\">\n",
+       "<ellipse fill=\"#ff0000\" fill-opacity=\"0.125490\" stroke=\"#ff0000\" stroke-opacity=\"0.125490\" cx=\"1136.5\" cy=\"-68\" rx=\"13\" ry=\"13\"/>\n",
+       "<text text-anchor=\"middle\" x=\"1136.5\" y=\"-64.9\" font-family=\"arial\" font-size=\"12.00\" fill=\"#7f0000\" fill-opacity=\"0.627451\">miniscope.ProcessingQualityMetrics</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Fluorescence&#45;&gt;miniscope.ProcessingQualityMetrics -->\n",
+       "<g id=\"edge8\" class=\"edge\">\n",
+       "<title>miniscope.Fluorescence-&gt;miniscope.ProcessingQualityMetrics</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M950.59,-129.56C985.94,-118.05 1088.85,-84.52 1124.32,-72.97\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.RecordingLocation -->\n",
+       "<g id=\"node6\" class=\"node\">\n",
+       "<title>miniscope.RecordingLocation</title>\n",
+       "<g id=\"a_node6\"><a xlink:title=\"→ miniscope.Recording\r------------------------------\r→ `neuro_reference`.`anatomical_location`\r\">\n",
+       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\" points=\"1041.5,-498 865.5,-498 865.5,-463 1041.5,-463 1041.5,-498\"/>\n",
+       "<text text-anchor=\"middle\" x=\"953.5\" y=\"-477.4\" font-family=\"arial\" font-size=\"12.00\" fill=\"darkgreen\">miniscope.RecordingLocation</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.ProcessingTask -->\n",
+       "<g id=\"node7\" class=\"node\">\n",
+       "<title>miniscope.ProcessingTask</title>\n",
+       "<g id=\"a_node7\"><a xlink:title=\"→ miniscope.RecordingInfo\r→ miniscope.ProcessingParamSet\r------------------------------\rprocessing_output_dir \rtask_mode=&quot;load&quot;     \r\">\n",
+       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\" points=\"1110,-427 951,-427 951,-392 1110,-392 1110,-427\"/>\n",
+       "<text text-anchor=\"middle\" x=\"1030.5\" y=\"-406.4\" font-family=\"arial\" font-size=\"12.00\" fill=\"darkgreen\">miniscope.ProcessingTask</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Processing -->\n",
+       "<g id=\"node31\" class=\"node\">\n",
+       "<title>miniscope.Processing</title>\n",
+       "<g id=\"a_node31\"><a xlink:title=\"→ miniscope.ProcessingTask\r------------------------------\rprocessing_time      \rpackage_version=&quot;&quot;   \r\">\n",
+       "<ellipse fill=\"#ff0000\" fill-opacity=\"0.125490\" stroke=\"#ff0000\" stroke-opacity=\"0.125490\" cx=\"1030.5\" cy=\"-343\" rx=\"13\" ry=\"13\"/>\n",
+       "<text text-anchor=\"middle\" x=\"1030.5\" y=\"-339.9\" font-family=\"arial\" font-size=\"12.00\" fill=\"#7f0000\" fill-opacity=\"0.627451\">miniscope.Processing</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.ProcessingTask&#45;&gt;miniscope.Processing -->\n",
+       "<g id=\"edge9\" class=\"edge\">\n",
+       "<title>miniscope.ProcessingTask-&gt;miniscope.Processing</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M1030.5,-391.89C1030.5,-380.69 1030.5,-366.17 1030.5,-356.07\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.MaskClassification -->\n",
+       "<g id=\"node8\" class=\"node\">\n",
+       "<title>miniscope.MaskClassification</title>\n",
+       "<g id=\"a_node8\"><a xlink:title=\"→ miniscope.Segmentation\r→ miniscope.MaskClassificationMethod\r\">\n",
+       "<ellipse fill=\"#ff0000\" fill-opacity=\"0.125490\" stroke=\"#ff0000\" stroke-opacity=\"0.125490\" cx=\"1357.5\" cy=\"-134.5\" rx=\"13\" ry=\"13\"/>\n",
+       "<text text-anchor=\"middle\" x=\"1357.5\" y=\"-131.4\" font-family=\"arial\" font-size=\"12.00\" fill=\"#7f0000\" fill-opacity=\"0.627451\">miniscope.MaskClassification</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.MaskClassification.MaskType -->\n",
+       "<g id=\"node32\" class=\"node\">\n",
+       "<title>miniscope.MaskClassification.MaskType</title>\n",
+       "<g id=\"a_node32\"><a xlink:title=\"→ miniscope.MaskClassification\r→ miniscope.Segmentation.Mask\r------------------------------\r→ miniscope.MaskType\rconfidence=null      \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"1455,-77.5 1260,-77.5 1260,-58.5 1455,-58.5 1455,-77.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"1357.5\" y=\"-65.5\" font-family=\"arial\" font-size=\"10.00\">miniscope.MaskClassification.MaskType</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.MaskClassification&#45;&gt;miniscope.MaskClassification.MaskType -->\n",
+       "<g id=\"edge10\" class=\"edge\">\n",
+       "<title>miniscope.MaskClassification-&gt;miniscope.MaskClassification.MaskType</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M1357.5,-121.37C1357.5,-108.67 1357.5,-89.04 1357.5,-77.77\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.MotionCorrection.Block -->\n",
+       "<g id=\"node9\" class=\"node\">\n",
+       "<title>miniscope.MotionCorrection.Block</title>\n",
+       "<g id=\"a_node9\"><a xlink:title=\"→ miniscope.MotionCorrection.NonRigidMotionCorrection\rblock_id             \r------------------------------\rblock_y              \rblock_x              \ry_shifts             \rx_shifts             \ry_std                \rx_std                \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"668.5,-19 502.5,-19 502.5,0 668.5,0 668.5,-19\"/>\n",
+       "<text text-anchor=\"start\" x=\"510.5\" y=\"-8\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.MotionCorrection.Block</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.MotionCorrection.Summary -->\n",
+       "<g id=\"node11\" class=\"node\">\n",
+       "<title>miniscope.MotionCorrection.Summary</title>\n",
+       "<g id=\"a_node11\"><a xlink:title=\"→ miniscope.MotionCorrection\r------------------------------\rref_image=null       \raverage_image        \rcorrelation_image=null \rmax_proj_image=null  \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"183,-77.5 0,-77.5 0,-58.5 183,-58.5 183,-77.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"91.5\" y=\"-65.5\" font-family=\"arial\" font-size=\"10.00\">miniscope.MotionCorrection.Summary</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Curation -->\n",
+       "<g id=\"node12\" class=\"node\">\n",
+       "<title>miniscope.Curation</title>\n",
+       "<g id=\"a_node12\"><a xlink:title=\"→ miniscope.Processing\rcuration_id          \r------------------------------\rcuration_time        \rcuration_output_dir  \rmanual_curation      \rcuration_note=&quot;&quot;     \r\">\n",
+       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\" points=\"1090.5,-294 970.5,-294 970.5,-259 1090.5,-259 1090.5,-294\"/>\n",
+       "<text text-anchor=\"start\" x=\"978.5\" y=\"-274.4\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"12.00\" fill=\"darkgreen\">miniscope.Curation</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Curation&#45;&gt;miniscope.MotionCorrection -->\n",
+       "<g id=\"edge11\" class=\"edge\">\n",
+       "<title>miniscope.Curation-&gt;miniscope.MotionCorrection</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M1014.34,-258.81C993.13,-238.13 953.74,-203.68 912.5,-188 867.41,-170.86 572.31,-150.75 416.51,-141.15\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Segmentation -->\n",
+       "<g id=\"node29\" class=\"node\">\n",
+       "<title>miniscope.Segmentation</title>\n",
+       "<g id=\"a_node29\"><a xlink:title=\"→ miniscope.Curation\r\">\n",
+       "<ellipse fill=\"#ff0000\" fill-opacity=\"0.125490\" stroke=\"#ff0000\" stroke-opacity=\"0.125490\" cx=\"1105.5\" cy=\"-205.5\" rx=\"13\" ry=\"13\"/>\n",
+       "<text text-anchor=\"middle\" x=\"1105.5\" y=\"-202.4\" font-family=\"arial\" font-size=\"12.00\" fill=\"#7f0000\" fill-opacity=\"0.627451\">miniscope.Segmentation</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Curation&#45;&gt;miniscope.Segmentation -->\n",
+       "<g id=\"edge12\" class=\"edge\">\n",
+       "<title>miniscope.Curation-&gt;miniscope.Segmentation</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M1048.66,-258.8C1063.74,-244.92 1084.58,-225.75 1096.38,-214.89\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.RecordingInfo -->\n",
+       "<g id=\"node13\" class=\"node\">\n",
+       "<title>miniscope.RecordingInfo</title>\n",
+       "<g id=\"a_node13\"><a xlink:title=\"→ miniscope.Recording\r------------------------------\rnchannels            \rnframes              \rpx_height=null       \rpx_width=null        \rum_height=null       \rum_width=null        \rfps                  \rgain=null            \rspatial_downsample=1 \rled_power            \rtime_stamps          \rrecording_datetime=null \rrecording_duration=null \r\">\n",
+       "<ellipse fill=\"#00007f\" fill-opacity=\"0.250980\" stroke=\"#00007f\" stroke-opacity=\"0.250980\" cx=\"754.5\" cy=\"-480.5\" rx=\"93.25\" ry=\"17.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"754.5\" y=\"-477.4\" font-family=\"arial\" font-size=\"12.00\" fill=\"#00007f\" fill-opacity=\"0.627451\">miniscope.RecordingInfo</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.RecordingInfo&#45;&gt;miniscope.ProcessingTask -->\n",
+       "<g id=\"edge13\" class=\"edge\">\n",
+       "<title>miniscope.RecordingInfo-&gt;miniscope.ProcessingTask</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M808.04,-466.11C852.72,-454.94 916.59,-438.98 964.44,-427.02\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.RecordingInfo.File -->\n",
+       "<g id=\"node24\" class=\"node\">\n",
+       "<title>miniscope.RecordingInfo.File</title>\n",
+       "<g id=\"a_node24\"><a xlink:title=\"→ miniscope.RecordingInfo\rfile_id              \r------------------------------\rfile_path            \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"826,-419 683,-419 683,-400 826,-400 826,-419\"/>\n",
+       "<text text-anchor=\"start\" x=\"691\" y=\"-408\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.RecordingInfo.File</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.RecordingInfo&#45;&gt;miniscope.RecordingInfo.File -->\n",
+       "<g id=\"edge14\" class=\"edge\">\n",
+       "<title>miniscope.RecordingInfo-&gt;miniscope.RecordingInfo.File</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M754.5,-462.8C754.5,-449.08 754.5,-430.19 754.5,-419.27\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Activity&#45;&gt;miniscope.Activity.Trace -->\n",
+       "<g id=\"edge15\" class=\"edge\">\n",
+       "<title>miniscope.Activity-&gt;miniscope.Activity.Trace</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M788.5,-54.74C788.5,-43.97 788.5,-28.56 788.5,-19.06\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.AcquisitionSoftware -->\n",
+       "<g id=\"node15\" class=\"node\">\n",
+       "<title>miniscope.AcquisitionSoftware</title>\n",
+       "<g id=\"a_node15\"><a xlink:title=\"acq_software         \r\">\n",
+       "<polygon fill=\"#000000\" fill-opacity=\"0.125490\" stroke=\"transparent\" points=\"857,-640 706,-640 706,-605 857,-605 857,-640\"/>\n",
+       "<text text-anchor=\"start\" x=\"714\" y=\"-621\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.AcquisitionSoftware</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Recording -->\n",
+       "<g id=\"node21\" class=\"node\">\n",
+       "<title>miniscope.Recording</title>\n",
+       "<g id=\"a_node21\"><a xlink:title=\"→ session.Session\rrecording_id         \r------------------------------\r→ lab.Device\r→ miniscope.AcquisitionSoftware\rrecording_notes=&quot;&quot;   \r\">\n",
+       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\" points=\"919.5,-569 789.5,-569 789.5,-534 919.5,-534 919.5,-569\"/>\n",
+       "<text text-anchor=\"start\" x=\"797.5\" y=\"-549.4\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"12.00\" fill=\"darkgreen\">miniscope.Recording</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.AcquisitionSoftware&#45;&gt;miniscope.Recording -->\n",
+       "<g id=\"edge16\" class=\"edge\">\n",
+       "<title>miniscope.AcquisitionSoftware-&gt;miniscope.Recording</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-dasharray=\"5,2\" stroke-opacity=\"0.250980\" d=\"M799.17,-604.8C810.65,-593.95 825.55,-579.87 836.99,-569.05\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.MotionCorrection&#45;&gt;miniscope.MotionCorrection.Summary -->\n",
+       "<g id=\"edge17\" class=\"edge\">\n",
+       "<title>miniscope.MotionCorrection-&gt;miniscope.MotionCorrection.Summary</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M269.68,-119.19C224.35,-106.42 159.5,-88.15 121.82,-77.54\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.MotionCorrection.RigidMotionCorrection -->\n",
+       "<g id=\"node18\" class=\"node\">\n",
+       "<title>miniscope.MotionCorrection.RigidMotionCorrection</title>\n",
+       "<g id=\"a_node18\"><a xlink:title=\"→ miniscope.MotionCorrection\r------------------------------\routlier_frames=null  \ry_shifts             \rx_shifts             \ry_std                \rx_std                \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"439.5,-77.5 201.5,-77.5 201.5,-58.5 439.5,-58.5 439.5,-77.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"320.5\" y=\"-65.5\" font-family=\"arial\" font-size=\"10.00\">miniscope.MotionCorrection.RigidMotionCorrection</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.MotionCorrection&#45;&gt;miniscope.MotionCorrection.RigidMotionCorrection -->\n",
+       "<g id=\"edge18\" class=\"edge\">\n",
+       "<title>miniscope.MotionCorrection-&gt;miniscope.MotionCorrection.RigidMotionCorrection</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M320.5,-116.89C320.5,-104.35 320.5,-87.64 320.5,-77.64\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.MotionCorrection.NonRigidMotionCorrection -->\n",
+       "<g id=\"node20\" class=\"node\">\n",
+       "<title>miniscope.MotionCorrection.NonRigidMotionCorrection</title>\n",
+       "<g id=\"a_node20\"><a xlink:title=\"→ miniscope.MotionCorrection\r------------------------------\routlier_frames=null  \rblock_height         \rblock_width          \rblock_count_y        \rblock_count_x        \r\">\n",
+       "<polygon fill=\"transparent\" stroke=\"transparent\" points=\"713.5,-77.5 457.5,-77.5 457.5,-58.5 713.5,-58.5 713.5,-77.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"585.5\" y=\"-65.5\" font-family=\"arial\" font-size=\"10.00\">miniscope.MotionCorrection.NonRigidMotionCorrection</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.MotionCorrection&#45;&gt;miniscope.MotionCorrection.NonRigidMotionCorrection -->\n",
+       "<g id=\"edge19\" class=\"edge\">\n",
+       "<title>miniscope.MotionCorrection-&gt;miniscope.MotionCorrection.NonRigidMotionCorrection</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M377.02,-119.74C429.62,-106.94 506.34,-88.27 550.55,-77.51\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.ActivityExtractionMethod -->\n",
+       "<g id=\"node19\" class=\"node\">\n",
+       "<title>miniscope.ActivityExtractionMethod</title>\n",
+       "<g id=\"a_node19\"><a xlink:title=\"extraction_method    \r\">\n",
+       "<polygon fill=\"#000000\" fill-opacity=\"0.125490\" stroke=\"transparent\" points=\"808,-152 635,-152 635,-117 808,-117 808,-152\"/>\n",
+       "<text text-anchor=\"start\" x=\"643\" y=\"-133\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.ActivityExtractionMethod</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.ActivityExtractionMethod&#45;&gt;miniscope.Activity -->\n",
+       "<g id=\"edge20\" class=\"edge\">\n",
+       "<title>miniscope.ActivityExtractionMethod-&gt;miniscope.Activity</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M738.75,-116.89C751.78,-104.35 769.13,-87.64 779.52,-77.64\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.MotionCorrection.NonRigidMotionCorrection&#45;&gt;miniscope.MotionCorrection.Block -->\n",
+       "<g id=\"edge21\" class=\"edge\">\n",
+       "<title>miniscope.MotionCorrection.NonRigidMotionCorrection-&gt;miniscope.MotionCorrection.Block</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M585.5,-58.17C585.5,-47.5 585.5,-29.65 585.5,-19.08\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Recording&#45;&gt;miniscope.RecordingLocation -->\n",
+       "<g id=\"edge22\" class=\"edge\">\n",
+       "<title>miniscope.Recording-&gt;miniscope.RecordingLocation</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M878.21,-533.97C893.77,-523.13 914.05,-509 929.64,-498.13\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Recording&#45;&gt;miniscope.RecordingInfo -->\n",
+       "<g id=\"edge23\" class=\"edge\">\n",
+       "<title>miniscope.Recording-&gt;miniscope.RecordingInfo</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M830.55,-533.97C814.6,-522.97 793.75,-508.58 777.91,-497.65\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.ProcessingMethod -->\n",
+       "<g id=\"node22\" class=\"node\">\n",
+       "<title>miniscope.ProcessingMethod</title>\n",
+       "<g id=\"a_node22\"><a xlink:title=\"processing_method    \r------------------------------\rprocessing_method_desc=&quot;&quot; \r\">\n",
+       "<polygon fill=\"#000000\" fill-opacity=\"0.125490\" stroke=\"transparent\" points=\"1210,-569 1065,-569 1065,-534 1210,-534 1210,-569\"/>\n",
+       "<text text-anchor=\"start\" x=\"1073\" y=\"-550\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.ProcessingMethod</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.ProcessingParamSet -->\n",
+       "<g id=\"node25\" class=\"node\">\n",
+       "<title>miniscope.ProcessingParamSet</title>\n",
+       "<g id=\"a_node25\"><a xlink:title=\"paramset_idx         \r------------------------------\r→ miniscope.ProcessingMethod\rparamset_desc        \rparam_set_hash       \rparams               \rUNIQUE INDEX (param_set_hash)\r\">\n",
+       "<polygon fill=\"#000000\" fill-opacity=\"0.125490\" stroke=\"transparent\" points=\"1215.5,-498 1059.5,-498 1059.5,-463 1215.5,-463 1215.5,-498\"/>\n",
+       "<text text-anchor=\"start\" x=\"1067.5\" y=\"-479\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.ProcessingParamSet</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.ProcessingMethod&#45;&gt;miniscope.ProcessingParamSet -->\n",
+       "<g id=\"edge24\" class=\"edge\">\n",
+       "<title>miniscope.ProcessingMethod-&gt;miniscope.ProcessingParamSet</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-dasharray=\"5,2\" stroke-opacity=\"0.250980\" d=\"M1137.5,-533.8C1137.5,-522.95 1137.5,-508.87 1137.5,-498.05\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.MaskType -->\n",
+       "<g id=\"node23\" class=\"node\">\n",
+       "<title>miniscope.MaskType</title>\n",
+       "<g id=\"a_node23\"><a xlink:title=\"mask_type            \r\">\n",
+       "<polygon fill=\"#000000\" fill-opacity=\"0.125490\" stroke=\"transparent\" points=\"1572,-152 1463,-152 1463,-117 1572,-117 1572,-152\"/>\n",
+       "<text text-anchor=\"start\" x=\"1471\" y=\"-133\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.MaskType</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.MaskType&#45;&gt;miniscope.MaskClassification.MaskType -->\n",
+       "<g id=\"edge25\" class=\"edge\">\n",
+       "<title>miniscope.MaskType-&gt;miniscope.MaskClassification.MaskType</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-dasharray=\"5,2\" stroke-opacity=\"0.250980\" d=\"M1476.3,-116.89C1445.19,-104.35 1403.75,-87.64 1378.93,-77.64\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.ProcessingParamSet&#45;&gt;miniscope.ProcessingTask -->\n",
+       "<g id=\"edge26\" class=\"edge\">\n",
+       "<title>miniscope.ProcessingParamSet-&gt;miniscope.ProcessingTask</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M1111.87,-462.97C1095.05,-452.13 1073.14,-438 1056.29,-427.13\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Channel -->\n",
+       "<g id=\"node26\" class=\"node\">\n",
+       "<title>miniscope.Channel</title>\n",
+       "<g id=\"a_node26\"><a xlink:title=\"channel              \r\">\n",
+       "<polygon fill=\"#000000\" fill-opacity=\"0.125490\" stroke=\"transparent\" points=\"886.5,-294 786.5,-294 786.5,-259 886.5,-259 886.5,-294\"/>\n",
+       "<text text-anchor=\"start\" x=\"794.5\" y=\"-275\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.Channel</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.Channel&#45;&gt;0 -->\n",
+       "<g id=\"edge27\" class=\"edge\">\n",
+       "<title>miniscope.Channel-&gt;0</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M836.5,-258.8C836.5,-240.93 836.5,-214.29 836.5,-207.91\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Channel&#45;&gt;1 -->\n",
+       "<g id=\"edge28\" class=\"edge\">\n",
+       "<title>miniscope.Channel-&gt;1</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-dasharray=\"5,2\" stroke-opacity=\"0.250980\" d=\"M850.78,-258.8C866.06,-240.93 888.84,-214.29 894.29,-207.91\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Channel&#45;&gt;2 -->\n",
+       "<g id=\"edge29\" class=\"edge\">\n",
+       "<title>miniscope.Channel-&gt;2</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-dasharray=\"5,2\" stroke-opacity=\"0.250980\" d=\"M786.38,-262.92C712.02,-244.27 579.44,-211 563.15,-206.92\"/>\n",
+       "</g>\n",
+       "<!-- subject.Subject -->\n",
+       "<g id=\"node27\" class=\"node\">\n",
+       "<title>subject.Subject</title>\n",
+       "<g id=\"a_node27\"><a xlink:title=\"subject              \r------------------------------\rsubject_nickname=&quot;&quot;  \rsex                  \rsubject_birth_date   \rsubject_description=&quot;&quot; \r\">\n",
+       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\" points=\"976.5,-711 878.5,-711 878.5,-676 976.5,-676 976.5,-711\"/>\n",
+       "<text text-anchor=\"start\" x=\"886.5\" y=\"-691.4\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"12.00\" fill=\"darkgreen\">subject.Subject</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- session.Session -->\n",
+       "<g id=\"node30\" class=\"node\">\n",
+       "<title>session.Session</title>\n",
+       "<g id=\"a_node30\"><a xlink:title=\"→ subject.Subject\rsession_datetime     \r\">\n",
+       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\" points=\"979.5,-640 875.5,-640 875.5,-605 979.5,-605 979.5,-640\"/>\n",
+       "<text text-anchor=\"start\" x=\"883.5\" y=\"-620.4\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"12.00\" fill=\"darkgreen\">session.Session</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- subject.Subject&#45;&gt;session.Session -->\n",
+       "<g id=\"edge30\" class=\"edge\">\n",
+       "<title>subject.Subject-&gt;session.Session</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M927.5,-675.8C927.5,-664.95 927.5,-650.87 927.5,-640.05\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.ProcessingQualityMetrics&#45;&gt;miniscope.ProcessingQualityMetrics.Trace -->\n",
+       "<g id=\"edge31\" class=\"edge\">\n",
+       "<title>miniscope.ProcessingQualityMetrics-&gt;miniscope.ProcessingQualityMetrics.Trace</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M1136.5,-54.74C1136.5,-43.97 1136.5,-28.56 1136.5,-19.06\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Segmentation&#45;&gt;miniscope.Fluorescence -->\n",
+       "<g id=\"edge32\" class=\"edge\">\n",
+       "<title>miniscope.Segmentation-&gt;miniscope.Fluorescence</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"2\" stroke-opacity=\"0.250980\" d=\"M1093.76,-199.65C1063.17,-187.01 981.28,-153.17 950.45,-140.44\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Segmentation&#45;&gt;miniscope.MaskClassification -->\n",
+       "<g id=\"edge33\" class=\"edge\">\n",
+       "<title>miniscope.Segmentation-&gt;miniscope.MaskClassification</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M1118,-201.08C1161,-189.3 1302.56,-150.54 1345.23,-138.86\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Segmentation&#45;&gt;miniscope.Segmentation.Mask -->\n",
+       "<g id=\"edge34\" class=\"edge\">\n",
+       "<title>miniscope.Segmentation-&gt;miniscope.Segmentation.Mask</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M1105.5,-192.48C1105.5,-178.74 1105.5,-156.56 1105.5,-144.32\"/>\n",
+       "</g>\n",
+       "<!-- session.Session&#45;&gt;miniscope.Recording -->\n",
+       "<g id=\"edge35\" class=\"edge\">\n",
+       "<title>session.Session-&gt;miniscope.Recording</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M909.83,-604.8C898.35,-593.95 883.45,-579.87 872.01,-569.05\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Processing&#45;&gt;miniscope.Curation -->\n",
+       "<g id=\"edge36\" class=\"edge\">\n",
+       "<title>miniscope.Processing-&gt;miniscope.Curation</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M1030.5,-329.87C1030.5,-319.8 1030.5,-305.37 1030.5,-294.2\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Segmentation.Mask&#45;&gt;miniscope.Fluorescence.Trace -->\n",
+       "<g id=\"edge37\" class=\"edge\">\n",
+       "<title>miniscope.Segmentation.Mask-&gt;miniscope.Fluorescence.Trace</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M1083.32,-124.93C1051.38,-112.6 992.76,-89.96 960.77,-77.6\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.Segmentation.Mask&#45;&gt;miniscope.MaskClassification.MaskType -->\n",
+       "<g id=\"edge38\" class=\"edge\">\n",
+       "<title>miniscope.Segmentation.Mask-&gt;miniscope.MaskClassification.MaskType</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M1138.96,-124.93C1187.16,-112.6 1275.62,-89.96 1323.9,-77.6\"/>\n",
+       "</g>\n",
+       "<!-- miniscope.MaskClassificationMethod -->\n",
+       "<g id=\"node34\" class=\"node\">\n",
+       "<title>miniscope.MaskClassificationMethod</title>\n",
+       "<g id=\"a_node34\"><a xlink:title=\"mask_classification_method \r\">\n",
+       "<polygon fill=\"#000000\" fill-opacity=\"0.125490\" stroke=\"transparent\" points=\"1447,-223 1268,-223 1268,-188 1447,-188 1447,-223\"/>\n",
+       "<text text-anchor=\"start\" x=\"1276\" y=\"-204\" font-family=\"arial\" text-decoration=\"underline\" font-size=\"10.00\">miniscope.MaskClassificationMethod</text>\n",
+       "</a>\n",
+       "</g>\n",
+       "</g>\n",
+       "<!-- miniscope.MaskClassificationMethod&#45;&gt;miniscope.MaskClassification -->\n",
+       "<g id=\"edge39\" class=\"edge\">\n",
+       "<title>miniscope.MaskClassificationMethod-&gt;miniscope.MaskClassification</title>\n",
+       "<path fill=\"none\" stroke=\"#000000\" stroke-width=\"0.75\" stroke-opacity=\"0.250980\" d=\"M1357.5,-187.8C1357.5,-175.35 1357.5,-158.66 1357.5,-147.51\"/>\n",
+       "</g>\n",
+       "</g>\n",
+       "</svg>"
+      ],
+      "text/plain": [
+       "<datajoint.diagram.Diagram at 0x7f882ecbbd00>"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "(dj.Diagram(subject.Subject) + dj.Diagram(session.Session) + dj.Diagram(miniscope))"
    ]
@@ -207,18 +831,49 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "subject              : varchar(8)                   \n",
+      "---\n",
+      "subject_nickname=\"\"  : varchar(64)                  \n",
+      "sex                  : enum('M','F','U')            \n",
+      "subject_birth_date   : date                         \n",
+      "subject_description=\"\" : varchar(1024)                \n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "print(subject.Subject.describe())"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "# \n",
+       "subject              : varchar(8)                   # \n",
+       "---\n",
+       "subject_nickname=\"\"  : varchar(64)                  # \n",
+       "sex                  : enum('M','F','U')            # \n",
+       "subject_birth_date   : date                         # \n",
+       "subject_description=\"\" : varchar(1024)                # "
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "subject.Subject.heading"
    ]
@@ -235,9 +890,105 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "    \n",
+       "    <style type=\"text/css\">\n",
+       "        .Table{\n",
+       "            border-collapse:collapse;\n",
+       "        }\n",
+       "        .Table th{\n",
+       "            background: #A0A0A0; color: #ffffff; padding:4px; border:#f0e0e0 1px solid;\n",
+       "            font-weight: normal; font-family: monospace; font-size: 100%;\n",
+       "        }\n",
+       "        .Table td{\n",
+       "            padding:4px; border:#f0e0e0 1px solid; font-size:100%;\n",
+       "        }\n",
+       "        .Table tr:nth-child(odd){\n",
+       "            background: #ffffff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        .Table tr:nth-child(even){\n",
+       "            background: #f3f1ff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        /* Tooltip container */\n",
+       "        .djtooltip {\n",
+       "        }\n",
+       "        /* Tooltip text */\n",
+       "        .djtooltip .djtooltiptext {\n",
+       "            visibility: hidden;\n",
+       "            width: 120px;\n",
+       "            background-color: black;\n",
+       "            color: #fff;\n",
+       "            text-align: center;\n",
+       "            padding: 5px 0;\n",
+       "            border-radius: 6px;\n",
+       "            /* Position the tooltip text - see examples below! */\n",
+       "            position: absolute;\n",
+       "            z-index: 1;\n",
+       "        }\n",
+       "        #primary {\n",
+       "            font-weight: bold;\n",
+       "            color: black;\n",
+       "        }\n",
+       "        #nonprimary {\n",
+       "            font-weight: normal;\n",
+       "            color: white;\n",
+       "        }\n",
+       "\n",
+       "        /* Show the tooltip text when you mouse over the tooltip container */\n",
+       "        .djtooltip:hover .djtooltiptext {\n",
+       "            visibility: visible;\n",
+       "        }\n",
+       "    </style>\n",
+       "    \n",
+       "    <b></b>\n",
+       "        <div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
+       "        <table border=\"1\" class=\"Table\">\n",
+       "            <thead> <tr style=\"text-align: right;\"> <th> <div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">subject</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">subject_nickname</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">sex</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">subject_birth_date</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">subject_description</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div> </th> </tr> </thead>\n",
+       "            <tbody> <tr> <td>subject1</td>\n",
+       "<td></td>\n",
+       "<td>U</td>\n",
+       "<td>2023-01-01</td>\n",
+       "<td></td> </tr> </tbody>\n",
+       "        </table>\n",
+       "        \n",
+       "        <p>Total: 1</p></div>\n",
+       "        "
+      ],
+      "text/plain": [
+       "*subject     subject_nickna sex     subject_birth_ subject_descri\n",
+       "+----------+ +------------+ +-----+ +------------+ +------------+\n",
+       "subject1                    U       2023-01-01                   \n",
+       " (Total: 1)"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "subject.Subject.insert1(\n",
     "    dict(subject=\"subject1\", subject_birth_date=\"2023-01-01\", sex=\"U\")\n",
@@ -255,18 +1006,41 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "-> subject.Subject\n",
+      "session_datetime     : datetime                     \n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "print(session.Session.describe())"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "# \n",
+       "subject              : varchar(8)                   # \n",
+       "session_datetime     : datetime                     # "
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "session.Session.heading"
    ]
@@ -289,7 +1063,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -298,9 +1072,93 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "    \n",
+       "    <style type=\"text/css\">\n",
+       "        .Table{\n",
+       "            border-collapse:collapse;\n",
+       "        }\n",
+       "        .Table th{\n",
+       "            background: #A0A0A0; color: #ffffff; padding:4px; border:#f0e0e0 1px solid;\n",
+       "            font-weight: normal; font-family: monospace; font-size: 100%;\n",
+       "        }\n",
+       "        .Table td{\n",
+       "            padding:4px; border:#f0e0e0 1px solid; font-size:100%;\n",
+       "        }\n",
+       "        .Table tr:nth-child(odd){\n",
+       "            background: #ffffff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        .Table tr:nth-child(even){\n",
+       "            background: #f3f1ff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        /* Tooltip container */\n",
+       "        .djtooltip {\n",
+       "        }\n",
+       "        /* Tooltip text */\n",
+       "        .djtooltip .djtooltiptext {\n",
+       "            visibility: hidden;\n",
+       "            width: 120px;\n",
+       "            background-color: black;\n",
+       "            color: #fff;\n",
+       "            text-align: center;\n",
+       "            padding: 5px 0;\n",
+       "            border-radius: 6px;\n",
+       "            /* Position the tooltip text - see examples below! */\n",
+       "            position: absolute;\n",
+       "            z-index: 1;\n",
+       "        }\n",
+       "        #primary {\n",
+       "            font-weight: bold;\n",
+       "            color: black;\n",
+       "        }\n",
+       "        #nonprimary {\n",
+       "            font-weight: normal;\n",
+       "            color: white;\n",
+       "        }\n",
+       "\n",
+       "        /* Show the tooltip text when you mouse over the tooltip container */\n",
+       "        .djtooltip:hover .djtooltiptext {\n",
+       "            visibility: visible;\n",
+       "        }\n",
+       "    </style>\n",
+       "    \n",
+       "    <b></b>\n",
+       "        <div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
+       "        <table border=\"1\" class=\"Table\">\n",
+       "            <thead> <tr style=\"text-align: right;\"> <th> <div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">subject</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">session_datetime</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div> </th> </tr> </thead>\n",
+       "            <tbody> <tr> <td>subject1</td>\n",
+       "<td>2023-01-01 00:00:00</td> </tr> </tbody>\n",
+       "        </table>\n",
+       "        \n",
+       "        <p>Total: 1</p></div>\n",
+       "        "
+      ],
+      "text/plain": [
+       "*subject     *session_datet\n",
+       "+----------+ +------------+\n",
+       "subject1     2023-01-01 00:\n",
+       " (Total: 1)"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "session.Session.insert1(session_key)\n",
     "session.Session()"
@@ -322,9 +1180,97 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 13,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "    \n",
+       "    <style type=\"text/css\">\n",
+       "        .Table{\n",
+       "            border-collapse:collapse;\n",
+       "        }\n",
+       "        .Table th{\n",
+       "            background: #A0A0A0; color: #ffffff; padding:4px; border:#f0e0e0 1px solid;\n",
+       "            font-weight: normal; font-family: monospace; font-size: 100%;\n",
+       "        }\n",
+       "        .Table td{\n",
+       "            padding:4px; border:#f0e0e0 1px solid; font-size:100%;\n",
+       "        }\n",
+       "        .Table tr:nth-child(odd){\n",
+       "            background: #ffffff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        .Table tr:nth-child(even){\n",
+       "            background: #f3f1ff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        /* Tooltip container */\n",
+       "        .djtooltip {\n",
+       "        }\n",
+       "        /* Tooltip text */\n",
+       "        .djtooltip .djtooltiptext {\n",
+       "            visibility: hidden;\n",
+       "            width: 120px;\n",
+       "            background-color: black;\n",
+       "            color: #fff;\n",
+       "            text-align: center;\n",
+       "            padding: 5px 0;\n",
+       "            border-radius: 6px;\n",
+       "            /* Position the tooltip text - see examples below! */\n",
+       "            position: absolute;\n",
+       "            z-index: 1;\n",
+       "        }\n",
+       "        #primary {\n",
+       "            font-weight: bold;\n",
+       "            color: black;\n",
+       "        }\n",
+       "        #nonprimary {\n",
+       "            font-weight: normal;\n",
+       "            color: white;\n",
+       "        }\n",
+       "\n",
+       "        /* Show the tooltip text when you mouse over the tooltip container */\n",
+       "        .djtooltip:hover .djtooltiptext {\n",
+       "            visibility: visible;\n",
+       "        }\n",
+       "    </style>\n",
+       "    \n",
+       "    <b></b>\n",
+       "        <div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
+       "        <table border=\"1\" class=\"Table\">\n",
+       "            <thead> <tr style=\"text-align: right;\"> <th> <div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">subject</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">session_datetime</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">session_dir</p>\n",
+       "                            <span class=\"djtooltiptext\">Path to the data directory for a session</span>\n",
+       "                        </div> </th> </tr> </thead>\n",
+       "            <tbody> <tr> <td>subject1</td>\n",
+       "<td>2023-01-01 00:00:00</td>\n",
+       "<td>session1</td> </tr> </tbody>\n",
+       "        </table>\n",
+       "        \n",
+       "        <p>Total: 1</p></div>\n",
+       "        "
+      ],
+      "text/plain": [
+       "*subject     *session_datet session_dir   \n",
+       "+----------+ +------------+ +------------+\n",
+       "subject1     2023-01-01 00: session1      \n",
+       " (Total: 1)"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "session.SessionDirectory.insert1(dict(**session_key, session_dir=\"session1\"))\n",
     "session.SessionDirectory()"
@@ -335,26 +1281,55 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As the workflow diagram indicates, the tables in the `probe` schemas need to\n",
-    "contain data before the tables in the `ephys` schema accept any data. Let's\n",
-    "start by inserting into `probe.Probe`, a table containing metadata about a\n",
-    "multielectrode probe. "
+    "As the workflow diagram indicates, the first table in the `miniscope` schema is the `miniscope.Recording` table."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 16,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "-> session.Session\n",
+      "recording_id         : int                          \n",
+      "---\n",
+      "-> lab.Device\n",
+      "-> miniscope.AcquisitionSoftware\n",
+      "recording_notes=\"\"   : varchar(4095)                # free-notes\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
-    "print(miniscope.Recording.describe)"
+    "print(miniscope.Recording.describe())"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 15,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "# \n",
+       "subject              : varchar(8)                   # \n",
+       "session_datetime     : datetime                     # \n",
+       "recording_id         : int                          # \n",
+       "---\n",
+       "device               : varchar(32)                  # \n",
+       "acq_software         : varchar(24)                  # \n",
+       "recording_notes=\"\"   : varchar(4095)                # free-notes"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "miniscope.Recording.heading"
    ]
@@ -364,22 +1339,36 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The probe metadata is used by the downstream `ProbeInsertion` table which we\n",
-    "insert data into in the cells below:"
+    "As you can see from the `describe()` method, this lab contains a dependency on the `Device` table within the `lab` schema. Let's quickly insert a miniscope device before inserting into `miniscope.Recording`. "
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 17,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "# \n",
+       "device               : varchar(32)                  # \n",
+       "---\n",
+       "modality             : varchar(64)                  # \n",
+       "description=\"\"       : varchar(256)                 # "
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "lab.Device.heading"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -388,7 +1377,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -410,7 +1399,7 @@
     "\n",
     "### Automatically populate tables\n",
     "\n",
-    "`miniscope.MiniscopeRecordingInfo` is the first table in this pipeline that can be\n",
+    "`miniscope.RecordingInfo` is the first table in this pipeline that can be\n",
     "automatically populated using using the `populate()` method.\n",
     "\n",
     "In DataJoint, the `populate()` method is a powerful feature designed to fill tables based on the logic defined in the table's `make` method. Here's a breakdown of its functionality:\n",
@@ -419,36 +1408,261 @@
     "\n",
     "- **Dependency Resolution**: Before populating a table, `populate()` ensures all its dependencies are populated. This maintains the integrity and consistency of the data.\n",
     "\n",
-    "- **Part Tables**: If a table has part tables associated with it, calling `populate()` on the main table will also populate its part tables. This is especially useful in cases like `ephys.EphysRecording` and its part table `ephys.EphysRecording.EphysFile`, as they are closely linked in terms of data lineage.\n",
+    "- **Part Tables**: If a table has part tables associated with it, calling `populate()` on the main table will also populate its part tables. This is especially useful in cases like `miniscope.RecordingInfo` and its part table `miniscope.RecordingInfo.File`, as they are closely linked in terms of data lineage.\n",
     "\n",
     "- **Restriction**: The `populate()` method can be restricted to specific entries. For instance, by providing a `session_key`, we're ensuring the method only operates on the data relevant to that particular session. This is both efficient and avoids unnecessary operations.\n",
     "\n",
-    "In the upcoming cells, we'll make use of the `populate()` method to fill the `miniscope.MiniscopeRecordingInfo` table and its part table. Remember, while this operation is automated, it's essential to understand the underlying logic to ensure accurate and consistent data entry.\n"
+    "In the upcoming cells, we'll make use of the `populate()` method to fill the `miniscope.RecordingInfo` table and its part table. Remember, while this operation is automated, it's essential to understand the underlying logic to ensure accurate and consistent data entry.\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 20,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "    \n",
+       "    <style type=\"text/css\">\n",
+       "        .Table{\n",
+       "            border-collapse:collapse;\n",
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+       "        .Table tr:nth-child(even){\n",
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+       "        #primary {\n",
+       "            font-weight: bold;\n",
+       "            color: black;\n",
+       "        }\n",
+       "        #nonprimary {\n",
+       "            font-weight: normal;\n",
+       "            color: white;\n",
+       "        }\n",
+       "\n",
+       "        /* Show the tooltip text when you mouse over the tooltip container */\n",
+       "        .djtooltip:hover .djtooltiptext {\n",
+       "            visibility: visible;\n",
+       "        }\n",
+       "    </style>\n",
+       "    \n",
+       "    <b>Store metadata about recording</b>\n",
+       "        <div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
+       "        <table border=\"1\" class=\"Table\">\n",
+       "            <thead> <tr style=\"text-align: right;\"> <th> <div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">subject</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">session_datetime</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">recording_id</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">nchannels</p>\n",
+       "                            <span class=\"djtooltiptext\">number of channels</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">nframes</p>\n",
+       "                            <span class=\"djtooltiptext\">number of recorded frames</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">px_height</p>\n",
+       "                            <span class=\"djtooltiptext\">height in pixels</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">px_width</p>\n",
+       "                            <span class=\"djtooltiptext\">width in pixels</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">um_height</p>\n",
+       "                            <span class=\"djtooltiptext\">height in microns</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">um_width</p>\n",
+       "                            <span class=\"djtooltiptext\">width in microns</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">fps</p>\n",
+       "                            <span class=\"djtooltiptext\">(Hz) frames per second</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">gain</p>\n",
+       "                            <span class=\"djtooltiptext\">recording gain</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">spatial_downsample</p>\n",
+       "                            <span class=\"djtooltiptext\">e.g. 1, 2, 4, 8. 1 for no downsampling</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">led_power</p>\n",
+       "                            <span class=\"djtooltiptext\">LED power used in the given recording</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">time_stamps</p>\n",
+       "                            <span class=\"djtooltiptext\">time stamps of each frame</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">recording_datetime</p>\n",
+       "                            <span class=\"djtooltiptext\">datetime of the recording</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">recording_duration</p>\n",
+       "                            <span class=\"djtooltiptext\">(seconds) duration of the recording</span>\n",
+       "                        </div> </th> </tr> </thead>\n",
+       "            <tbody> <tr>  </tr> </tbody>\n",
+       "        </table>\n",
+       "        \n",
+       "        <p>Total: 0</p></div>\n",
+       "        "
+      ],
+      "text/plain": [
+       "*subject    *session_datet *recording_id  nchannels     nframes     px_height     px_width     um_height     um_width     fps     gain     spatial_downsa led_power     time_stamp recording_date recording_dura\n",
+       "+---------+ +------------+ +------------+ +-----------+ +---------+ +-----------+ +----------+ +-----------+ +----------+ +-----+ +------+ +------------+ +-----------+ +--------+ +------------+ +------------+\n",
+       "\n",
+       " (Total: 0)"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "miniscope.RecordingInfo()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 21,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "    \n",
+       "    <style type=\"text/css\">\n",
+       "        .Table{\n",
+       "            border-collapse:collapse;\n",
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+       "        .djtooltip .djtooltiptext {\n",
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+       "            width: 120px;\n",
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+       "            color: #fff;\n",
+       "            text-align: center;\n",
+       "            padding: 5px 0;\n",
+       "            border-radius: 6px;\n",
+       "            /* Position the tooltip text - see examples below! */\n",
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+       "            z-index: 1;\n",
+       "        }\n",
+       "        #primary {\n",
+       "            font-weight: bold;\n",
+       "            color: black;\n",
+       "        }\n",
+       "        #nonprimary {\n",
+       "            font-weight: normal;\n",
+       "            color: white;\n",
+       "        }\n",
+       "\n",
+       "        /* Show the tooltip text when you mouse over the tooltip container */\n",
+       "        .djtooltip:hover .djtooltiptext {\n",
+       "            visibility: visible;\n",
+       "        }\n",
+       "    </style>\n",
+       "    \n",
+       "    <b></b>\n",
+       "        <div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
+       "        <table border=\"1\" class=\"Table\">\n",
+       "            <thead> <tr style=\"text-align: right;\"> <th> <div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">subject</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">session_datetime</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">recording_id</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">file_id</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">file_path</p>\n",
+       "                            <span class=\"djtooltiptext\">relative to root data directory</span>\n",
+       "                        </div> </th> </tr> </thead>\n",
+       "            <tbody> <tr>  </tr> </tbody>\n",
+       "        </table>\n",
+       "        \n",
+       "        <p>Total: 0</p></div>\n",
+       "        "
+      ],
+      "text/plain": [
+       "*subject    *session_datet *recording_id  *file_id    file_path    \n",
+       "+---------+ +------------+ +------------+ +---------+ +-----------+\n",
+       "\n",
+       " (Total: 0)"
+      ]
+     },
+     "execution_count": 21,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "miniscope.RecordingInfo.File()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 22,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "RecordingInfo: 100%|██████████| 1/1 [00:01<00:00,  1.80s/it]\n"
+     ]
+    }
+   ],
    "source": [
     "miniscope.RecordingInfo.populate(session_key, display_progress=True)"
    ]
@@ -463,20 +1677,256 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 24,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "    \n",
+       "    <style type=\"text/css\">\n",
+       "        .Table{\n",
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+       "        .Table td{\n",
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+       "        .Table tr:nth-child(odd){\n",
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+       "        .djtooltip .djtooltiptext {\n",
+       "            visibility: hidden;\n",
+       "            width: 120px;\n",
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+       "        #primary {\n",
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+       "\n",
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+       "        .djtooltip:hover .djtooltiptext {\n",
+       "            visibility: visible;\n",
+       "        }\n",
+       "    </style>\n",
+       "    \n",
+       "    <b>Store metadata about recording</b>\n",
+       "        <div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
+       "        <table border=\"1\" class=\"Table\">\n",
+       "            <thead> <tr style=\"text-align: right;\"> <th> <div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">subject</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">session_datetime</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">recording_id</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">nchannels</p>\n",
+       "                            <span class=\"djtooltiptext\">number of channels</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">nframes</p>\n",
+       "                            <span class=\"djtooltiptext\">number of recorded frames</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">px_height</p>\n",
+       "                            <span class=\"djtooltiptext\">height in pixels</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">px_width</p>\n",
+       "                            <span class=\"djtooltiptext\">width in pixels</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">um_height</p>\n",
+       "                            <span class=\"djtooltiptext\">height in microns</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">um_width</p>\n",
+       "                            <span class=\"djtooltiptext\">width in microns</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">fps</p>\n",
+       "                            <span class=\"djtooltiptext\">(Hz) frames per second</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">gain</p>\n",
+       "                            <span class=\"djtooltiptext\">recording gain</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">spatial_downsample</p>\n",
+       "                            <span class=\"djtooltiptext\">e.g. 1, 2, 4, 8. 1 for no downsampling</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">led_power</p>\n",
+       "                            <span class=\"djtooltiptext\">LED power used in the given recording</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">time_stamps</p>\n",
+       "                            <span class=\"djtooltiptext\">time stamps of each frame</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">recording_datetime</p>\n",
+       "                            <span class=\"djtooltiptext\">datetime of the recording</span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">recording_duration</p>\n",
+       "                            <span class=\"djtooltiptext\">(seconds) duration of the recording</span>\n",
+       "                        </div> </th> </tr> </thead>\n",
+       "            <tbody> <tr> <td>subject1</td>\n",
+       "<td>2023-01-01 00:00:00</td>\n",
+       "<td>1</td>\n",
+       "<td>1</td>\n",
+       "<td>111770</td>\n",
+       "<td>600</td>\n",
+       "<td>600</td>\n",
+       "<td>nan</td>\n",
+       "<td>nan</td>\n",
+       "<td>20.0</td>\n",
+       "<td>2.0</td>\n",
+       "<td>1</td>\n",
+       "<td>5.0</td>\n",
+       "<td>=BLOB=</td>\n",
+       "<td>None</td>\n",
+       "<td>5588.5</td> </tr> </tbody>\n",
+       "        </table>\n",
+       "        \n",
+       "        <p>Total: 1</p></div>\n",
+       "        "
+      ],
+      "text/plain": [
+       "*subject     *session_datet *recording_id  nchannels     nframes     px_height     px_width     um_height     um_width     fps      gain     spatial_downsa led_power     time_stamp recording_date recording_dura\n",
+       "+----------+ +------------+ +------------+ +-----------+ +---------+ +-----------+ +----------+ +-----------+ +----------+ +------+ +------+ +------------+ +-----------+ +--------+ +------------+ +------------+\n",
+       "subject1     2023-01-01 00: 1              1             111770      600           600          nan           nan          20.0     2.0      1              5.0           =BLOB=     None           5588.5        \n",
+       " (Total: 1)"
+      ]
+     },
+     "execution_count": 24,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "miniscope.MiniscopeRecordingInfo()"
+    "miniscope.RecordingInfo()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 25,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "    \n",
+       "    <style type=\"text/css\">\n",
+       "        .Table{\n",
+       "            border-collapse:collapse;\n",
+       "        }\n",
+       "        .Table th{\n",
+       "            background: #A0A0A0; color: #ffffff; padding:4px; border:#f0e0e0 1px solid;\n",
+       "            font-weight: normal; font-family: monospace; font-size: 100%;\n",
+       "        }\n",
+       "        .Table td{\n",
+       "            padding:4px; border:#f0e0e0 1px solid; font-size:100%;\n",
+       "        }\n",
+       "        .Table tr:nth-child(odd){\n",
+       "            background: #ffffff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        .Table tr:nth-child(even){\n",
+       "            background: #f3f1ff;\n",
+       "            color: #000000;\n",
+       "        }\n",
+       "        /* Tooltip container */\n",
+       "        .djtooltip {\n",
+       "        }\n",
+       "        /* Tooltip text */\n",
+       "        .djtooltip .djtooltiptext {\n",
+       "            visibility: hidden;\n",
+       "            width: 120px;\n",
+       "            background-color: black;\n",
+       "            color: #fff;\n",
+       "            text-align: center;\n",
+       "            padding: 5px 0;\n",
+       "            border-radius: 6px;\n",
+       "            /* Position the tooltip text - see examples below! */\n",
+       "            position: absolute;\n",
+       "            z-index: 1;\n",
+       "        }\n",
+       "        #primary {\n",
+       "            font-weight: bold;\n",
+       "            color: black;\n",
+       "        }\n",
+       "        #nonprimary {\n",
+       "            font-weight: normal;\n",
+       "            color: white;\n",
+       "        }\n",
+       "\n",
+       "        /* Show the tooltip text when you mouse over the tooltip container */\n",
+       "        .djtooltip:hover .djtooltiptext {\n",
+       "            visibility: visible;\n",
+       "        }\n",
+       "    </style>\n",
+       "    \n",
+       "    <b></b>\n",
+       "        <div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
+       "        <table border=\"1\" class=\"Table\">\n",
+       "            <thead> <tr style=\"text-align: right;\"> <th> <div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">subject</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">session_datetime</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">recording_id</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"primary\">file_id</p>\n",
+       "                            <span class=\"djtooltiptext\"></span>\n",
+       "                        </div></th><th><div class=\"djtooltip\">\n",
+       "                            <p id=\"nonprimary\">file_path</p>\n",
+       "                            <span class=\"djtooltiptext\">relative to root data directory</span>\n",
+       "                        </div> </th> </tr> </thead>\n",
+       "            <tbody> <tr> <td>subject1</td>\n",
+       "<td>2023-01-01 00:00:00</td>\n",
+       "<td>1</td>\n",
+       "<td>0</td>\n",
+       "<td>session1/0.avi</td> </tr> </tbody>\n",
+       "        </table>\n",
+       "        \n",
+       "        <p>Total: 1</p></div>\n",
+       "        "
+      ],
+      "text/plain": [
+       "*subject     *session_datet *recording_id  *file_id    file_path     \n",
+       "+----------+ +------------+ +------------+ +---------+ +------------+\n",
+       "subject1     2023-01-01 00: 1              0           session1/0.avi\n",
+       " (Total: 1)"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "miniscope.MiniscopeRecordingInfo.File()"
+    "miniscope.RecordingInfo.File()"
    ]
   },
   {
@@ -496,51 +1946,93 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 26,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "# Parameter set used for processing of miniscope data\n",
+       "paramset_idx         : smallint                     # \n",
+       "---\n",
+       "processing_method    : varchar(16)                  # \n",
+       "paramset_desc        : varchar(128)                 # \n",
+       "param_set_hash       : uuid                         # \n",
+       "params               : longblob                     # dictionary of all applicable parameters"
+      ]
+     },
+     "execution_count": 26,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "miniscope.ProcessingParamSet.heading"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 27,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'ephys' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[27], line 26\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[39m# insert clustering task manually\u001b[39;00m\n\u001b[1;32m      2\u001b[0m params_ks \u001b[39m=\u001b[39m {\n\u001b[1;32m      3\u001b[0m     \u001b[39m\"\u001b[39m\u001b[39mfs\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m30000\u001b[39m,\n\u001b[1;32m      4\u001b[0m     \u001b[39m\"\u001b[39m\u001b[39mfshigh\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m150\u001b[39m,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     24\u001b[0m     \u001b[39m\"\u001b[39m\u001b[39museRAM\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m0\u001b[39m,\n\u001b[1;32m     25\u001b[0m }\n\u001b[0;32m---> 26\u001b[0m ephys\u001b[39m.\u001b[39mClusteringParamSet\u001b[39m.\u001b[39minsert_new_params(\n\u001b[1;32m     27\u001b[0m     clustering_method\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mkilosort2\u001b[39m\u001b[39m\"\u001b[39m,\n\u001b[1;32m     28\u001b[0m     paramset_idx\u001b[39m=\u001b[39m\u001b[39m0\u001b[39m,\n\u001b[1;32m     29\u001b[0m     params\u001b[39m=\u001b[39mparams_ks,\n\u001b[1;32m     30\u001b[0m     paramset_desc\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mSpike sorting using Kilosort2\u001b[39m\u001b[39m\"\u001b[39m,\n\u001b[1;32m     31\u001b[0m )\n\u001b[1;32m     32\u001b[0m ephys\u001b[39m.\u001b[39mClusteringParamSet()\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'ephys' is not defined"
+     ]
+    }
+   ],
    "source": [
-    "# insert clustering task manually\n",
-    "params_ks = {\n",
-    "    \"fs\": 30000,\n",
-    "    \"fshigh\": 150,\n",
-    "    \"minfr_goodchannels\": 0.1,\n",
-    "    \"Th\": [10, 4],\n",
-    "    \"lam\": 10,\n",
-    "    \"AUCsplit\": 0.9,\n",
-    "    \"minFR\": 0.02,\n",
-    "    \"momentum\": [20, 400],\n",
-    "    \"sigmaMask\": 30,\n",
-    "    \"ThPr\": 8,\n",
-    "    \"spkTh\": -6,\n",
-    "    \"reorder\": 1,\n",
-    "    \"nskip\": 25,\n",
-    "    \"GPU\": 1,\n",
-    "    \"Nfilt\": 1024,\n",
-    "    \"nfilt_factor\": 4,\n",
-    "    \"ntbuff\": 64,\n",
-    "    \"whiteningRange\": 32,\n",
-    "    \"nSkipCov\": 25,\n",
-    "    \"scaleproc\": 200,\n",
-    "    \"nPCs\": 3,\n",
-    "    \"useRAM\": 0,\n",
-    "}\n",
-    "ephys.ClusteringParamSet.insert_new_params(\n",
-    "    clustering_method=\"kilosort2\",\n",
-    "    paramset_idx=0,\n",
-    "    params=params_ks,\n",
-    "    paramset_desc=\"Spike sorting using Kilosort2\",\n",
+    "params = dict(\n",
+    "    decay_time=0.4,\n",
+    "    pw_rigid=False,\n",
+    "    max_shifts=(5, 5),\n",
+    "    gSig_filt=(3, 3),\n",
+    "    strides=(48, 48),\n",
+    "    overlaps=(24, 24),\n",
+    "    max_deviation_rigid=3,\n",
+    "    border_nan=\"copy\",\n",
+    "    method_init=\"corr_pnr\",\n",
+    "    K=None,\n",
+    "    gSig=(3, 3),\n",
+    "    gSiz=(13, 13),\n",
+    "    merge_thr=0.7,\n",
+    "    p=1,\n",
+    "    tsub=2,\n",
+    "    ssub=1,\n",
+    "    rf=40,\n",
+    "    stride=20,\n",
+    "    only_init=True,\n",
+    "    nb=0,\n",
+    "    nb_patch=0,\n",
+    "    method_deconvolution=\"oasis\",\n",
+    "    low_rank_background=None,\n",
+    "    update_background_components=True,\n",
+    "    min_corr=0.8,\n",
+    "    min_pnr=10,\n",
+    "    normalize_init=False,\n",
+    "    center_psf=True,\n",
+    "    ssub_B=2,\n",
+    "    ring_size_factor=1.4,\n",
+    "    del_duplicates=True,\n",
+    "    border_pix=0,\n",
+    "    min_SNR=3,\n",
+    "    rval_thr=0.85,\n",
+    "    use_cnn=False,\n",
     ")\n",
-    "ephys.ClusteringParamSet()"
+    "\n",
+    "\n",
+    "miniscope.ProcessingParamSet.insert_new_params(\n",
+    "    processing_method=\"caiman\",\n",
+    "    paramset_id=0,\n",
+    "    paramset_desc=\"Miniscope analysis with CaImAn using default parameters\",\n",
+    "    params=params,\n",
+    ")"
    ]
   },
   {
@@ -548,9 +2040,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now that we've inserted kilosort parameters into the `ClusteringParamSet` table,\n",
-    "we're almost ready to sort our data. DataJoint uses a `ClusteringTask` table to\n",
-    "manage which `EphysRecording` and `ClusteringParamSet` should be used during processing. \n",
+    "Now that we've inserted kilosort parameters into the `ProcessingParamSet` table,\n",
+    "we're almost ready to run image processing. DataJoint uses a `ProcessingTask` table to\n",
+    "manage which `Recording` and `ProcessingParamSet` should be used during processing. \n",
     "\n",
     "This table is important for defining several important aspects of\n",
     "downstream processing. Let's view the attributes to get a better understanding. "
@@ -558,11 +2050,29 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 28,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "# Manual table marking a processing task to be triggered or manually processed\n",
+       "subject              : varchar(8)                   # \n",
+       "session_datetime     : datetime                     # \n",
+       "recording_id         : int                          # \n",
+       "paramset_idx         : smallint                     # \n",
+       "---\n",
+       "processing_output_dir : varchar(255)                 # relative to the root data directory\n",
+       "task_mode=\"load\"     : enum('load','trigger')       # 'load': load existing results"
+      ]
+     },
+     "execution_count": 28,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "ephys.ClusteringTask.heading"
+    "miniscope.ProcessingTask.heading"
    ]
   },
   {
@@ -570,14 +2080,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The `ClusteringTask` table contains two important attributes: \n",
-    "+ `paramset_idx` \n",
+    "The `ProcessingTask` table contains two important attributes: \n",
+    "+ `paramset_id` \n",
     "+ `task_mode` \n",
     "\n",
-    "The `paramset_idx` attribute tracks\n",
+    "The `paramset_id` attribute tracks\n",
     "your kilosort parameter sets. You can choose the parameter set using which \n",
-    "you want spike sort ephys data. For example, `paramset_idx=0` may contain\n",
-    "default parameters for kilosort processing whereas `paramset_idx=1` contains your custom parameters for sorting. This\n",
+    "you want spike sort ephys data. For example, `paramset_id=0` may contain\n",
+    "default parameters for kilosort processing whereas `paramset_id=1` contains your custom parameters for sorting. This\n",
     "attribute tells the `Processing` table which set of parameters you are processing in a given `populate()`.\n",
     "\n",
     "The `task_mode` attribute can be set to either `load` or `trigger`. When set to `load`,\n",
@@ -591,13 +2101,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ephys.ClusteringTask.insert1(\n",
+    "miniscope.ProcessingTask.insert1(\n",
     "    dict(\n",
-    "        session_key,\n",
-    "        insertion_number=1,\n",
-    "        paramset_idx=0,\n",
+    "        **session_key,\n",
+    "        recording_id=1,\n",
+    "        paramset_id=0,\n",
     "        task_mode=\"load\",  # load or trigger\n",
-    "        clustering_output_dir=\"processed/subject5/session1/probe_1/kilosort2-5_1\",\n",
+    "        processing_output_dir=\"session1\",\n",
     "    )\n",
     ")"
    ]
@@ -608,7 +2118,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ephys.Clustering.populate(session_key, display_progress=True)"
+    "miniscope.Processing.populate(session_key, display_progress=True)"
    ]
   },
   {
@@ -627,7 +2137,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ephys.Curation.heading"
+    "miniscope.Curation.heading"
    ]
   },
   {
@@ -636,8 +2146,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "clustering_key = (ephys.ClusteringTask & session_key).fetch1(\"KEY\")\n",
-    "ephys.Curation().create1_from_clustering_task(clustering_key)"
+    "clustering_key = (miniscope.ProcessingTask & session_key).fetch1(\"KEY\")\n",
+    "miniscope.Curation().create1_from_clustering_task(clustering_key)"
    ]
   },
   {
@@ -655,9 +2165,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ephys.CuratedClustering.populate(session_key, display_progress=True)\n",
-    "ephys.LFP.populate(session_key, display_progress=True)\n",
-    "ephys.WaveformSet.populate(session_key, display_progress=True)"
+    "miniscope.CuratedClustering.populate(session_key, display_progress=True)\n",
+    "miniscope.MotionCorrection.populate(session_key, display_progress=True)\n",
+    "miniscope.Segmentation.populate(session_key, display_progress=True)\n",
+    "miniscope.Fluorescence.populate(session_key, display_progress=True)\n",
+    "miniscope.Activity.populate(session_key, display_progress=True)"
    ]
   },
   {