diff --git a/Docker/SPACEc_cpu b/Docker/SPACEc_cpu
index d56aa88..61cdc8f 100644
--- a/Docker/SPACEc_cpu
+++ b/Docker/SPACEc_cpu
@@ -1,5 +1,5 @@
-# Start from a base CUDA image
-FROM ubuntu:20.04
+# Start from a base image
+FROM debian:bullseye-slim
 
 # Update the package list
 RUN apt-get update && \
@@ -41,19 +41,21 @@ RUN conda run pip install spacec
 RUN conda run pip install "TissUUmaps" && \
     conda install libxml2=2.9.10 && \
     conda run pip install torch_geometric && \
-    conda run pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.3.0+cu121.html && \
+    conda run pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.3.0+cu121.html
 
 
 # Copy notebooks into a new directory in the Docker image
 COPY notebooks /notebooks
-COPY example_data /example_data
 
 # Set the new directory as the working directory
 WORKDIR /notebooks
 
+# Clean up to reduce image size
+RUN conda clean -afy
+
 # Expose Jupyter port
 EXPOSE 8888
 EXPOSE 5100
 
 # Set the default command to run Jupyter
-CMD ["conda", "run", "-n", "spacec", "jupyter", "notebook", "--ip='0.0.0.0'", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token=''"]
+CMD ["conda", "run", "-n", "spacec", "jupyter", "notebook", "--ip='0.0.0.0'", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token=''"]
\ No newline at end of file
diff --git a/Docker/SPACEc_gpu b/Docker/SPACEc_gpu
index e3a16c5..988feda 100644
--- a/Docker/SPACEc_gpu
+++ b/Docker/SPACEc_gpu
@@ -49,7 +49,6 @@ RUN conda run pip install "TissUUmaps" && \
 
 # Copy notebooks into a new directory in the Docker image
 COPY notebooks /notebooks
-COPY example_data /example_data
 
 # Set the new directory as the working directory
 WORKDIR /notebooks
diff --git a/Docker/old/Dockerfile b/Docker/old/Dockerfile
deleted file mode 100755
index a040805..0000000
--- a/Docker/old/Dockerfile
+++ /dev/null
@@ -1,94 +0,0 @@
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-ARG OWNER=jupyter
-ARG BASE_CONTAINER=$OWNER/r-notebook
-FROM $BASE_CONTAINER
-
-LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
-
-# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
-# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
-SHELL ["/bin/bash", "-o", "pipefail", "-c"]
-
-USER root
-
-RUN apt-get update --yes && \
-    apt-get install --yes --no-install-recommends \
-    # for cython: https://cython.readthedocs.io/en/latest/src/quickstart/install.html
-    build-essential \
-    # for latex labels
-    cm-super \
-    dvipng \
-    # for matplotlib anim
-    ffmpeg && \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
-
-USER ${NB_UID}
-
-# Install Python 3 packages
-RUN mamba install --yes \
-    'altair' \
-    'beautifulsoup4' \
-    'bokeh' \
-    'bottleneck' \
-    'cloudpickle' \
-    'conda-forge::blas=*=openblas' \
-    'cython' \
-    'dask' \
-    'dill' \
-    'h5py' \
-    'ipympl'\
-    'ipywidgets' \
-    'jupyter_server>=2.0.0' \
-    'jupyterlab-git' \
-    'matplotlib-base=3.6.3' \
-    'numba=0.55.2' \
-    'numexpr' \
-    'numpy=1.22.3' \
-    'openpyxl' \
-    'pandas=1.5.3' \
-    'patsy' \
-    'protobuf' \
-    'pytables' \
-	'tensorly' \
-	'scanpy' \
-    'scikit-image' \
-    'scikit-learn' \
-    'scipy' \
-    'seaborn=0.12.2' \
-    'sqlalchemy' \
-    'statsmodels=0.13.5' \
-    'sympy' \
-    'widgetsnbextension'\
-    'yellowbrick=1.5' \
-    "graphviz" \
-    "pydot" \
-    "pygraphviz" \
-    'xlrd' && \
-    mamba clean --all -f -y && \
-    fix-permissions "${CONDA_DIR}" && \
-    fix-permissions "/home/${NB_USER}"
-
-# Install facets which does not have a pip or conda package at the moment
-WORKDIR /tmp
-RUN git clone https://github.com/PAIR-code/facets.git && \
-    jupyter nbextension install facets/facets-dist/ --sys-prefix && \
-    rm -rf /tmp/facets && \
-    fix-permissions "${CONDA_DIR}" && \
-    fix-permissions "/home/${NB_USER}"
-
-# Import matplotlib the first time to build the font cache.
-ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/"
-
-RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
-    fix-permissions "/home/${NB_USER}"
-
-RUN NotebookApp.iopub_data_rate_limit=1.0e10
-
-WORKDIR "${HOME}"
-
-
-COPY SAP_helperfunctions_hf.py .
-COPY SAP_preprocessing_pp.py .
-COPY SAP_tools_tl.py .
-COPY SAP_plot_pl.py .
diff --git a/Docker/old/tutorial.Dockerfile b/Docker/old/tutorial.Dockerfile
deleted file mode 100644
index 692cc2b..0000000
--- a/Docker/old/tutorial.Dockerfile
+++ /dev/null
@@ -1,66 +0,0 @@
-ARG BASE_IMAGE=ubuntu:22.04
-FROM ${BASE_IMAGE}
-
-# install packages
-RUN apt-get -y update --allow-releaseinfo-change\
-    && apt-get -y autoremove \
-    && apt-get clean \
-    && apt-get install -y \
-    fonts-liberation \
-    locales \
-    wget curl \
-    unzip \
-    # - bzip2 is necessary to extract the micromamba executable.
-    bzip2 \
-    # - pandoc is used to convert notebooks to html files
-    #   it's not present in aarch64 ubuntu image, so we install it here
-    pandoc \
-    git \
-    vim \
-    zsh \
-    tmux \
-    build-essential \
-    gcc \
-    # clean up
-    && rm -fr /var/lib/apt/lists/* /tmp/* /var/tmp/* \
-    && echo "en_US.UTF-8 UTF-8" > /etc/locale.gen \
-    && locale-gen
-
-# TODO: not really sure why I need this
-ENV LC_ALL=en_US.UTF-8 \
-    LANG=en_US.UTF-8 \
-    LANGUAGE=en_US.UTF-8
-
-# install and setup micromamba
-ENV MAMBA_ROOT_PREFIX=/opt/mamba
-RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba \
-   && /bin/micromamba shell init -s zsh -p ${MAMBA_ROOT_PREFIX} \
-   && echo "alias mamba=micromamba" >> ~/.zshrc
-ENV MAMBA_EXEC=/bin/micromamba
-
-ARG ENV_NAME="SPACEc"
-RUN ${MAMBA_EXEC} env create -n ${ENV_NAME} -c conda-forge python=3.10 jupyterlab
-
-# install python packages
-ARG GITHUB_USER
-ARG GITHUB_TOKEN
-RUN ${MAMBA_EXEC} run -n ${ENV_NAME} pip install --no-cache-dir \
-    git+https://${GITHUB_USER}:${GITHUB_TOKEN}@github.com/yuqiyuqitan/SAP.git@preppip
-
-
-# download tutorial files and run jupyterlab on startup
-
-ENV ENV_NAME=${ENV_NAME}
-EXPOSE 8888
-
-# attempt to fix situation by running with -u $UID
-# but then new files end up with weird permissions: drwxr-Sr--+
-# probably could be done easier with some MAMBA path change
-#RUN \
-#  mkdir -p /.cache/mamba; chmod -R 777 /.cache; \
-#  mkdir /.local; chmod 777 /.local; \
-#  mkdir /.jupyter; chmod 777 /.jupyter;
-
-WORKDIR /workspace
-COPY tutorial_init.sh /
-CMD ["bash", "/tutorial_init.sh"]
diff --git a/Docker/old/tutorial_init.sh b/Docker/old/tutorial_init.sh
deleted file mode 100644
index 9d4da6b..0000000
--- a/Docker/old/tutorial_init.sh
+++ /dev/null
@@ -1,44 +0,0 @@
-echo
-echo "Starting SpacCodEx environment"
-echo "=============================="
-
-# TODO: tryin to fix issue with extracted files keeing ids from inside the archive
-#echo "Setup for user: ${RUN_UID}"
-#useradd --uid ${RUN_UID} spacec
-#mkdir /home/spacec
-#chown -R spacec:spacec /home/spacec
-#chown -R ${RUN_ID}:${RUN_ID} /workspace
-
-echo "Checking tutorial materials."
-cd /workspace
-
-# if data and notebook folder do not exist
-if [ ! -d "/workspace/data" ] && [ ! -d "/workspace/notebooks" ]; then
-	echo "Data and notebooks for the tutorial are missing."
-	read -p "Do you want to download the tutorial materials? [y/n] " -n 1 -r
-	echo
-	if [[ ! $REPLY =~ ^[Yy]$ ]]; then
-		echo "Skipping download."
-	else
-		echo
-		echo "Downloading tutorial materials:"
-		wget -O materials.zip "https://www.dropbox.com/scl/fo/qxgrxq6y7y2jlrwhotabd/h?rlkey=3rp5cjkkrexnfxkqbtgr7l3h6&dl=1"
-		unzip materials.zip
-		rm materials.zip
-		echo
-		echo "Downloading model:"
-		mkdir -p notebooks/models/Mesmer_model
-		cd notebooks/models/Mesmer_model
-		wget -O model.tar.gz "https://deepcell-data.s3-us-west-1.amazonaws.com/saved-models/MultiplexSegmentation-9.tar.gz"
-		tar -xzvf model.tar.gz
-		rm model.tar.gz
-		chown -R ${UID}:${UID} .
-		cd -
-	fi
-else
-	echo "Data and notebooks folders for the tutorial are present. Skipping download."
-fi
-
-echo
-echo "Starting Jupyter Lab:"
-${MAMBA_EXEC} run -n ${ENV_NAME} jupyter lab --allow-root --NotebookApp.token="" --ip="*"