diff --git a/README.md b/README.md
index 94d589b..c6dc4a1 100644
--- a/README.md
+++ b/README.md
@@ -64,7 +64,7 @@ transcriptome.save('../tests/data/example_1_isotools.pkl')
 
 ## Citation and feedback
 
-* If you run into any issues, please use the [github issues report feature](https://github.com/HerwigLab/IsoTools2/issues).
+* If you run into any issues, please use the [github issues](https://github.com/HerwigLab/IsoTools2/issues) report feature.
 * For general feedback, please write us an email to [yalan_bi@molgen.mpg.de](mailto:yalan_bi@molgen.mpg.de) and [herwig@molgen.mpg.de](mailto:herwig@molgen.mpg.de).
 * If you use IsoTools in your publication, please cite the following paper in addition to this repository:
   * Lienhard, Matthias et al. “**IsoTools: a flexible workflow for long-read transcriptome sequencing analysis**.” Bioinformatics (Oxford, England) vol. 39,6 (2023): btad364. [doi:10.1093/bioinformatics/btad364](https://doi.org/10.1093/bioinformatics/btad364)
diff --git a/docs/notebooks/ENCODE_S2.ipynb b/docs/notebooks/ENCODE_S2.ipynb
index 067f46f..5b76a87 100644
--- a/docs/notebooks/ENCODE_S2.ipynb
+++ b/docs/notebooks/ENCODE_S2.ipynb
@@ -9,8 +9,20 @@
     "This tutorial guides through a typical Long Read Transcriptome Sequencing (LRTS) analysis workflow with isotools, \n",
     "using ENCODE Isoseq Sequel2 Data. It demonstrates the analysis of alternative splicing events within and between sample groups. \n",
     "\n",
-    "The original analysis integrates quite a large number of samples, and consequently runs several hours. Users interested in reproducing the notebook should consider restricting the data to the samples they are interested in.\n",
-    "\n",
+    "The original analysis integrates quite a large number of samples, and consequently runs several hours. Users interested in reproducing the notebook should consider restricting the data to the samples they are interested in."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Note:** This case study was analysed with the old version 0.2.7 of IsoTools and has not been updated to reflect the current API and output conventions."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "## Preparation\n",
     "In this notebook, \"long read RNA-seq\" samples are downloaded from ENCODE to the \"encode\" subdirectory. You can also manually download the files using the data portal (https://www.encodeproject.org/) and download aligned .bam files. Here I use all Sequel II samples leukemia and b-cell samples the time of writing, but you can choose to process a subset. \n",
     "\n",
diff --git a/docs/notebooks/Isotools_overview.png b/docs/notebooks/Isotools_overview.png
new file mode 100644
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diff --git a/docs/notebooks/Isotools_overview_slide.png b/docs/notebooks/Isotools_overview_slide.png
deleted file mode 100644
index 86ca9d2..0000000
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diff --git a/docs/notebooks/isotools_alzheimer.ipynb b/docs/notebooks/isotools_alzheimer.ipynb
index 5a41133..aa1901c 100644
--- a/docs/notebooks/isotools_alzheimer.ipynb
+++ b/docs/notebooks/isotools_alzheimer.ipynb
@@ -6,8 +6,20 @@
    "source": [
     "# Case Study: PacBio 2019 Alzheimer Sequel2 dataset\n",
     "\n",
-    "This notebook demonstrates the data preprocessing, import and basic vizualization of genes with Sashimi plots. As it is based on a full sized isoseq dataset, it involves some preparation, and takes several hours to complete. For a smaller example, please check the test data notebook on the [github page](https://github.com/MatthiasLienhard/isotools/blob/master/notebooks/test_data.ipynb).\n",
-    "\n",
+    "This notebook demonstrates the data preprocessing, import and basic vizualization of genes with Sashimi plots. As it is based on a full sized isoseq dataset, it involves some preparation, and takes several hours to complete. For a smaller example, please check the test data notebook on the [github page](https://github.com/MatthiasLienhard/isotools/blob/master/notebooks/test_data.ipynb)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Note:** This case study was analysed with the old version 0.2.8 of IsoTools and has not been updated to reflect the current API and output conventions."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "## Preparation\n",
     "1) Prepare the working directory and download the reference and data\n",
     "``` bash\n",
@@ -46,7 +58,8 @@
     "    ref='reference/GRCh38.p13.genome.fa'\n",
     "    pbmm2 align ${ref} alzheimer/flnc/${sample}_flnc.bam alzheimer/aligned/${sample}_aligned.sorted.bam --preset ISOSEQ --sort -j $n_threads \n",
     "```\n",
-    "\n"
+    "\n",
+    ""
    ]
   },
   {
diff --git a/docs/notebooks/isotools_diffsplice.png b/docs/notebooks/isotools_diffsplice.png
index aad9021..64d14e9 100644
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diff --git a/docs/quickstart.rst b/docs/quickstart.rst
index 93510df..140d0c3 100644
--- a/docs/quickstart.rst
+++ b/docs/quickstart.rst
@@ -16,7 +16,7 @@ Key features:
 * Support for proteogenomic approaches at the interface of transcriptomics and proteomics.
 * Various data visualizations.
 
-.. image:: notebooks/Isotools_overview_slide.png
+.. image:: notebooks/Isotools_overview.png
   :width: 800
   :alt: IsoTools overview