diff --git a/_toc.yml b/_toc.yml
index fc7f3da..9e30516 100644
--- a/_toc.yml
+++ b/_toc.yml
@@ -2,10 +2,6 @@ format: jb-book
 root: README
 
 parts:
-  - caption: Setup
-    chapters:
-    - file: "download_data.ipynb"
-
   - caption: Verification
     chapters:
     - file: "notebooks/verification.ipynb"
@@ -14,9 +10,3 @@ parts:
     chapters:
     - file: "notebooks/mean_traces.ipynb"
     - file: "notebooks/filtering.ipynb"
-
-  - caption: Appendix
-    chapters:
-    - file: "notebooks/reference_frame.ipynb"
-    - file: "notebooks/spacing.ipynb"
-    - file: "notebooks/motion_fl.ipynb"
diff --git a/notebooks/motion_fl.ipynb b/notebooks/motion_fl.ipynb
deleted file mode 100644
index cf2dc95..0000000
--- a/notebooks/motion_fl.ipynb
+++ /dev/null
@@ -1,43 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "9193f62f-0b86-443f-b1c1-4126745dcf39",
-   "metadata": {},
-   "source": [
-    "# Motion from Fluorescence\n",
-    "\n",
-    "TBW"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "9f87e7bc-64ee-414d-ba69-e7e46c8622af",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.4"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
diff --git a/notebooks/reference_frame.ipynb b/notebooks/reference_frame.ipynb
deleted file mode 100644
index 25a43d0..0000000
--- a/notebooks/reference_frame.ipynb
+++ /dev/null
@@ -1,43 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "5307bce5-cc5c-4f8d-921b-55163e8e8395",
-   "metadata": {},
-   "source": [
-    "# Reference frame\n",
-    "\n",
-    "TBW"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1b897b77-475d-4889-ac9e-48081586703c",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.4"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
diff --git a/notebooks/spacing.ipynb b/notebooks/spacing.ipynb
deleted file mode 100644
index 4a6a411..0000000
--- a/notebooks/spacing.ipynb
+++ /dev/null
@@ -1,43 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "5b4ed12b-c34b-4ab0-821b-e40a8f72857d",
-   "metadata": {},
-   "source": [
-    "# Image spacing\n",
-    "\n",
-    "TBW"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "af0b0a05-4791-4fed-8e1a-763aff663fd1",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.4"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}