CosciaLab · josenimo · Jul 8, 2025 · Jul 8, 2025 · Jul 8, 2025
diff --git a/docs/Tutorials/T1_ImageAnalysis.ipynb b/docs/Tutorials/T1_ImageAnalysis.ipynb
diff --git a/docs/Tutorials/T2_ProteomicsIntegration.ipynb b/docs/Tutorials/T2_ProteomicsIntegration.ipynb
@@ -1,13 +1,5 @@
 {
  "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "a44cbb39",
-   "metadata": {},
-   "source": [
-    "# Integrating proteomics and imaging data"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "e07c2e72",

diff --git a/docs/Tutorials/T3_DownstreamProteomics.ipynb b/docs/Tutorials/T3_DownstreamProteomics.ipynb
diff --git a/docs/Tutorials/index.md b/docs/Tutorials/index.md
@@ -2,28 +2,29 @@
 
 This section provides hands-on tutorials to guide you through the core workflows of `openDVP`. Each tutorial uses our demo dataset and covers a key aspect of a Deep Visual Proteomics analysis.
 
-### Tutorial 1: Image Analysis
+## Tutorial 1: Image Analysis
 
 Learn the fundamentals of processing and analyzing high-plex immunofluorescence images. This tutorial covers essential steps like quality control, cell segmentation, and feature extraction to prepare your imaging data for integration.
 
-### Tutorial 2: Integration of Imaging with Proteomics
+## Tutorial 2: Integration of Imaging with Proteomics
+
 Discover how to link your imaging-derived cellular data with quantitative proteomics measurements. This tutorial leverages `SpatialData` to create a unified data object, enabling powerful spatial-omics analysis.
 
-### Tutorial 3: Downstream Proteomics Analysis
+## Tutorial 3: Downstream Proteomics Analysis
+
 Dive into the analysis of your integrated proteomics data. This tutorial walks you through common downstream tasks such as data normalization, identifying cell populations, and performing differential abundance analysis to uncover biological insights.
 
-## Tutorials
+## Tutorial links
 
 - [Tutorial 1: Image analysis](T1_ImageAnalysis)
 - [Tutorial 2: Integration of imaging with proteomics](T2_ProteomicsIntegration)
 - [Tutorial 3: Downstream proteomics analysis](T3_DownstreamProteomics)
 
-
 ```{toctree}
 :maxdepth: 2
 :hidden:
 
 T1_ImageAnalysis
 T2_ProteomicsIntegration
 T3_DownstreamProteomics
-```
+```
diff --git a/docs/Tutorials/old/T1_ImageAnalysis.ipynb b/docs/Tutorials/old/T1_ImageAnalysis.ipynb