Update 1_compute-summary-motility-metrics.ipynb (#33)

Make a variety of small improvements:
- better wording
- update links
- update paths

notebooks/1_compute-summary-motility-metrics.ipynb

@@ -11,11 +11,11 @@
     "#### Overview\n",
     "This notebook computes summary motility metrics from individual cell trajectories that were extracted from time lapse microscopy data acquired across two different imaging experiments.\n",
     "\n",
-    "_Idea is that this notebook generates datasets for the subsequent notebooks so that you don't have to go through the trouble of downloading the dataset to work with the summary motility metrics._\n",
+    "_The idea is that this notebook generates datasets for the subsequent notebooks so that you don't have to go through the trouble of downloading the dataset to work with the summary motility metrics. I.e. running this notebook is not a prerequisite for the subsequent notebooks._\n",
     "\n",
     "Details regarding the imaging experiments, the motility metrics, and the procedure for extracting cell trajectories from the time-lapse microscopy data can be found in the [pub](https://doi.org/10.57844/arcadia-2d61-fb05). The cell trajectories are stored in CSV files that can be found in the BioImage Archive [data repository](https://doi.org/10.6019/S-BIAD1298).\n",
     "\n",
-    "This notebook outputs two CSV files to [`data/`](../data), one for each imaging experiment. The columns of the CSV file are the various motility metrics (total distance, net distance, confinement ratio, etc.), and each row corresponds to the summary motility metrics for one particular cell trajectory. Only the motility metrics for trajectories longer than 20µm and with a duration lasting more than 10s are output to the CSV file. Because the time lapses are 20s, this ensures that cells are not represented more than once.\n",
+    "This notebook outputs two CSV files to [`data/`](../data), one for each imaging experiment. The columns of the CSV file are the various motility metrics (total distance, net distance, confinement ratio, etc.), and each row corresponds to the summary motility metrics for one particular cell trajectory. Only the motility metrics for trajectories longer than 20 µm and with a duration lasting more than 10 s are output to the CSV file. Because the time lapses are 20 s, this ensures that cells are not represented more than once.\n",
     "\n",
     "Note that cell trajectories were originally output by running the script [`../src/chlamytracker/scripts/track_cells.py`](../src/chlamytracker/scripts/track_cells.py).\n",
     "\n",
@@ -54,7 +54,7 @@
    "metadata": {},
    "source": [
     "#### Collect CSV files\n",
-    "As stated above, the cell trajectories are stored in CSV files that can be found in the [data repository]() [*add link*]. The file paths in `input_directories` should be updated to wherever this data has been downloaded to."
+    "As stated above, the cell trajectories are stored in CSV files that can be found in the [data repository](https://doi.org/10.6019/S-BIAD1298). The file paths in `input_directories` should be updated to wherever this data has been downloaded to."
    ]
   },
   {
@@ -78,10 +78,10 @@
    "source": [
     "input_directories = {\n",
     "    \"AMID-04\": Path(\n",
-    "        \"/Volumes/Microscopy/Published_Datasets/HTP-motility-assay/AMID-04_Pools_cc124\"\n",
+    "        \"/Volumes/Microscopy/Published_Datasets/resource-HTP-swimming-assay/AMID-04_CC-124_pools\"\n",
     "    ),\n",
     "    \"AMID-05\": Path(\n",
-    "        \"/Volumes/Microscopy/Published_Datasets/HTP-motility-assay/AMID-05_Wells_cc124\"\n",
+    "        \"/Volumes/Microscopy/Published_Datasets/resource-HTP-swimming-assay/AMID-05_CC-124_wells\"\n",
     "    ),\n",
     "}\n",
     "\n",
@@ -206,7 +206,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "00332c5171fb4e91b0e214945113df36",
+       "model_id": "568db33c94b94534ae69524672303070",
        "version_major": 2,
        "version_minor": 0
       },
@@ -220,7 +220,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "7b6611a3c6a94205a74e0fd761b5aa91",
+       "model_id": "1f6f86e34cde4797b0a2bdcf6ff700eb",
        "version_major": 2,
        "version_minor": 0
       },