diff --git a/MSUtils/TPMS/__init__.py b/MSUtils/TPMS/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/MSUtils/TPMS/tpms.py b/MSUtils/TPMS/tpms.py
new file mode 100644
index 0000000..957522a
--- /dev/null
+++ b/MSUtils/TPMS/tpms.py
@@ -0,0 +1,298 @@
+import numpy as np
+from typing import Iterable, Optional
+
+from MSUtils.general.MicrostructureImage import MicrostructureImage
+from MSUtils.general.h52xdmf import write_xdmf
+
+
+def _to_angle(x, L):
+    return (x / L) * 2.0 * np.pi
+
+
+class TPMS:
+    """
+    TPMS generator.
+
+    Parameters
+    ----------
+    tpms_type : str
+        Type of TPMS surface (e.g., 'gyroid', 'schwarz_p', 'diamond', 'neovius', 'iwp', 'lidinoid').
+    resolution : tuple of int
+        Number of voxels in each direction (Nx, Ny, Nz).
+    L : tuple of float
+        Physical size in each direction (Lx, Ly, Lz).
+    threshold : float
+        Level-set value at which to threshold the implicit function.
+    unitcell_frequency : tuple of int
+        Number of unit cell repeats in each direction.
+    invert : bool
+        If True, swap the solid/void assignment (invert phases).
+    mode : str
+        'solid' (default) for classic TPMS, 'shell' for a shell of finite thickness.
+    shell_thickness : float
+        If mode='shell', the thickness of the shell (in field units, not physical units).
+    """
+
+    def __init__(
+        self,
+        tpms_type,
+        resolution: Optional[Iterable[int]] = (128, 128, 128),
+        L: Optional[Iterable[float]] = (1.0, 1.0, 1.0),
+        threshold: Optional[float] = 0.5,
+        unitcell_frequency: Optional[Iterable[int]] = (1, 1, 1),
+        invert: bool = False,
+        mode: str = "solid",
+        shell_thickness: float = 0.1,
+    ):
+        self.kind = tpms_type.lower()
+        self.resolution = tuple(int(v) for v in resolution)
+        self.L = tuple(float(v) for v in L)
+        if isinstance(unitcell_frequency, int):
+            unitcell_frequency = (
+                unitcell_frequency,
+                unitcell_frequency,
+                unitcell_frequency,
+            )
+        self.frequency = tuple(int(v) for v in unitcell_frequency)
+        self.threshold = threshold
+        self.invert = invert
+        self.mode = mode
+        self.shell_thickness = shell_thickness
+
+        self._field = None  # cache for field
+        self.image = self.generate()
+
+    def implicit_function(
+        self, x: np.ndarray, y: np.ndarray, z: np.ndarray
+    ) -> np.ndarray:
+        # Map by frequency: scale coordinates before mapping to angle
+        kx, ky, kz = self.frequency
+        X = _to_angle(x * kx, self.L[0])
+        Y = _to_angle(y * ky, self.L[1])
+        Z = _to_angle(z * kz, self.L[2])
+
+        kind = self.kind
+        # Standard references: https://minimalsurfaces.blog/home/repository/triply-periodic/
+        #                      https://kenbrakke.com/evolver/examples/periodic/periodic.html
+        if kind in ("gyroid",):
+            # Gyroid: sin(x)cos(y) + sin(y)cos(z) + sin(z)cos(x)
+            return np.sin(X) * np.cos(Y) + np.sin(Y) * np.cos(Z) + np.sin(Z) * np.cos(X)
+        if kind in ("schwarz_p", "p"):
+            # Schwarz Primitive: cos(x) + cos(y) + cos(z)
+            return np.cos(X) + np.cos(Y) + np.cos(Z)
+        if kind in ("schwarz_d", "diamond", "d"):
+            # Diamond: sin(x)sin(y)sin(z) + sin(x)cos(y)cos(z) + cos(x)sin(y)cos(z) + cos(x)cos(y)sin(z)
+            return (
+                np.sin(X) * np.sin(Y) * np.sin(Z)
+                + np.sin(X) * np.cos(Y) * np.cos(Z)
+                + np.cos(X) * np.sin(Y) * np.cos(Z)
+                + np.cos(X) * np.cos(Y) * np.sin(Z)
+            )
+        if kind in ("neovius",):
+            # Neovius: 3 * (cos(x) + cos(y) + cos(z)) + 4 * cos(x)*cos(y)*cos(z)
+            return 3 * (np.cos(X) + np.cos(Y) + np.cos(Z)) + 4 * np.cos(X) * np.cos(
+                Y
+            ) * np.cos(Z)
+        if kind in ("iwp"):
+            # I-WP : 2 * (cos(x)cos(y) + cos(y)cos(z) + cos(z)cos(x)) - (cos(2x) + cos(2y) + cos(2z))
+            return 2 * (
+                np.cos(X) * np.cos(Y) + np.cos(Y) * np.cos(Z) + np.cos(Z) * np.cos(X)
+            ) - (np.cos(2 * X) + np.cos(2 * Y) + np.cos(2 * Z))
+        if kind in ("lidinoid",):
+            # Lidinoid: 0.5 * (sin(2x)cos(y)sin(z) + sin(2y)cos(z)sin(x) + sin(2z)cos(x)sin(y)) - 0.5 * (cos(2x)cos(2y) + cos(2y)cos(2z) + cos(2z)cos(2x)) + 0.15
+            return (
+                0.5
+                * (
+                    np.sin(2 * X) * np.cos(Y) * np.sin(Z)
+                    + np.sin(2 * Y) * np.cos(Z) * np.sin(X)
+                    + np.sin(2 * Z) * np.cos(X) * np.sin(Y)
+                )
+                - 0.5
+                * (
+                    np.cos(2 * X) * np.cos(2 * Y)
+                    + np.cos(2 * Y) * np.cos(2 * Z)
+                    + np.cos(2 * Z) * np.cos(2 * X)
+                )
+                + 0.15
+            )
+        raise ValueError(f"Unknown or unsupported TPMS kind: {self.kind}")
+
+    def _compute_field(self):
+        # Compute and cache the field
+        Nx, Ny, Nz = self.resolution
+        Lx, Ly, Lz = self.L
+        xs = np.linspace(0.0, Lx, Nx, endpoint=False)
+        ys = np.linspace(0.0, Ly, Ny, endpoint=False)
+        zs = np.linspace(0.0, Lz, Nz, endpoint=False)
+        X = xs[:, None, None]
+        Y = ys[None, :, None]
+        Z = zs[None, None, :]
+        self._field = self.implicit_function(X, Y, Z)
+        # range normalize to [0, 1]
+        self._field = (self._field - np.min(self._field)) / (
+            np.max(self._field) - np.min(self._field)
+        )
+        return self._field
+
+    def generate(self, threshold: Optional[float] = None) -> np.ndarray:
+        """
+        Generate the binary microstructure.
+        Returns a 3D numpy array (1=solid, 0=void). If invert=True, phases are swapped.
+        If mode='shell', produces a shell of given thickness (in field units).
+        """
+        if self._field is None:
+            field = self._compute_field()
+        else:
+            field = self._field
+        if threshold is None:
+            threshold = self.threshold
+        if self.mode == "solid":
+            img = (field > threshold).astype(np.uint8)
+        elif self.mode == "shell":
+            t = abs(self.shell_thickness)
+            img = (np.abs(field - threshold) < t).astype(np.uint8)
+        else:
+            raise ValueError(f"Unknown mode: {self.mode}")
+        if self.invert:
+            img = 1 - img
+        return img
+
+    def find_threshold_for_volume_fraction(
+        self,
+        target_vf: float,
+        tol: float = 1e-3,
+        max_iter: int = 30,
+        n_thresh: int = 50,
+        optimize: str = "both",
+    ) -> tuple:
+        """
+        Find threshold (and shell thickness if mode='shell') for target volume fraction.
+        Parameters:
+            target_vf: target volume fraction (fraction of solid voxels)
+            tol: tolerance for volume fraction
+            max_iter: max iterations for bisection
+            n_thresh: number of threshold samples (for shell mode, if optimizing threshold)
+            optimize: 'threshold', 'shell_thickness', or 'both' (shell mode only)
+                - 'threshold': optimize threshold, keep shell_thickness fixed
+                - 'shell_thickness': optimize shell_thickness, keep threshold fixed
+                - 'both': jointly optimize both (default)
+        Returns:
+            - solid mode: (threshold, None)
+            - shell mode: (threshold, shell_thickness)
+        """
+        if self._field is None:
+            field = self._compute_field()
+        else:
+            field = self._field
+        flat = field.ravel()
+        n_vox = flat.size
+        if self.mode == "solid":
+            # For solid: threshold at quantile
+            k = int(np.round((1 - target_vf) * n_vox))
+            sorted_field = np.partition(flat, k)
+            thr = sorted_field[k]
+            self.threshold = thr
+            return thr, None
+        elif self.mode == "shell":
+            minf, maxf = float(np.min(flat)), float(np.max(flat))
+            if optimize == "shell_thickness":
+                # Only optimize shell_thickness, keep threshold fixed
+                thr = self.threshold
+                lo, hi = 0.0, max(maxf - thr, thr - minf)
+                for _ in range(max_iter):
+                    mid = 0.5 * (lo + hi)
+                    vf = np.mean(np.abs(flat - thr) < mid)
+                    err = abs(vf - target_vf)
+                    if err < tol:
+                        break
+                    if vf > target_vf:
+                        hi = mid
+                    else:
+                        lo = mid
+                self.shell_thickness = mid
+                return thr, mid
+            elif optimize == "threshold":
+                # Only optimize threshold, keep shell_thickness fixed
+                t = abs(self.shell_thickness)
+                best_err = float("inf")
+                best_thr = None
+                for thr in np.linspace(minf, maxf, n_thresh):
+                    vf = np.mean(np.abs(flat - thr) < t)
+                    err = abs(vf - target_vf)
+                    if err < best_err:
+                        best_err = err
+                        best_thr = thr
+                        if best_err <= tol:
+                            break
+                self.threshold = best_thr
+                return best_thr, t
+            elif optimize == "both":
+                # Jointly optimize threshold and shell_thickness
+                best_err = float("inf")
+                best_thr = None
+                best_t = None
+                for thr in np.linspace(minf, maxf, n_thresh):
+                    lo, hi = 0.0, max(maxf - thr, thr - minf)
+                    for _ in range(max_iter):
+                        mid = 0.5 * (lo + hi)
+                        vf = np.mean(np.abs(flat - thr) < mid)
+                        err = abs(vf - target_vf)
+                        if err < tol:
+                            break
+                        if vf > target_vf:
+                            hi = mid
+                        else:
+                            lo = mid
+                    vf = np.mean(np.abs(flat - thr) < mid)
+                    err = abs(vf - target_vf)
+                    if err < best_err:
+                        best_err = err
+                        best_thr = thr
+                        best_t = mid
+                        if best_err <= tol:
+                            break
+                self.threshold = best_thr
+                self.shell_thickness = best_t
+                return best_thr, best_t
+            else:
+                raise ValueError(f"Unknown optimize mode: {optimize}")
+        else:
+            raise ValueError(f"Unknown mode: {self.mode}")
+
+
+def main():
+    N = 512, 256, 128
+    L = 4.0, 2.0, 1.0
+    tpms_types = ["gyroid", "schwarz_p", "diamond", "neovius", "iwp", "lidinoid"]
+    h5_filename = "data/tpms.h5"
+    unitcell_frequency = (4, 2, 1)
+    invert = True
+
+    for tpms_type in tpms_types:
+        tpms = TPMS(
+            tpms_type=tpms_type,
+            resolution=N,
+            L=L,
+            unitcell_frequency=unitcell_frequency,
+            invert=invert,
+            mode="solid",
+        )
+        MS = MicrostructureImage(image=tpms.image)
+        MS.write(
+            h5_filename=h5_filename,
+            dset_name=tpms_type,
+            order="zyx",
+            compression_level=9,
+        )
+
+    write_xdmf(
+        h5_filepath=h5_filename,
+        xdmf_filepath="data/tpms.xdmf",
+        microstructure_length=L[::-1],
+        time_series=False,
+        verbose=True,
+    )
+
+
+if __name__ == "__main__":
+    main()
diff --git a/MSUtils/TPMS/tpms_example.py b/MSUtils/TPMS/tpms_example.py
new file mode 100644
index 0000000..6d5c532
--- /dev/null
+++ b/MSUtils/TPMS/tpms_example.py
@@ -0,0 +1,77 @@
+"""
+Example script demonstrating the generation and optimization of a Triply Periodic Minimal Surface (TPMS) microstructure.
+This script creates a TPMS microstructure of type 'iwp' in shell mode with specified resolution and dimensions.
+It first generates an initial microstructure, computes volume fractions, and writes it to an HDF5 file.
+Then, it optimizes the shell thickness to achieve a target volume fraction of 0.2 for phase 0,
+regenerates the microstructure with optimized parameters, recomputes volume fractions, and writes the optimized
+result to HDF5.
+"""
+from MSUtils.TPMS.tpms import TPMS
+from MSUtils.general.MicrostructureImage import MicrostructureImage
+from MSUtils.general.h52xdmf import write_xdmf
+
+if __name__ == "__main__":
+    N = 256, 256, 256
+    L = 1.0, 1.0, 1.0
+    tpms_type = "iwp"
+    h5_filename = "data/tpms_opt.h5"
+    unitcell_frequency = (1, 1, 1)
+    invert = False
+
+    tpms = TPMS(
+        tpms_type=tpms_type,
+        resolution=N,
+        L=L,
+        unitcell_frequency=unitcell_frequency,
+        invert=invert,
+        mode="shell",
+        shell_thickness=0.1,
+    )
+    MS = MicrostructureImage(image=tpms.image)
+    print(f"Volume fraction of phase 0: {MS.volume_fractions[0]:.4f}")
+    print(f"Volume fraction of phase 1: {MS.volume_fractions[1]:.4f}")
+    MS.write(
+        h5_filename=h5_filename,
+        dset_name="threshold_opt/" + tpms_type + "_thresh_0",
+        order="zyx",
+        compression_level=9,
+    )
+
+    # Optimize shell thickness to achieve target volume fraction for phase 1
+    vf_target_phase_1 = 0.2
+    threshold_opt, thickness_opt = tpms.find_threshold_for_volume_fraction(
+        vf_target_phase_1, optimize="shell_thickness"
+    )
+    print(
+        f"New threshold and shell thickness for volume fraction {vf_target_phase_1}: {threshold_opt}, {thickness_opt}"
+    )
+
+    # Regenerate TPMS with optimized parameters
+    tpms = TPMS(
+        tpms_type=tpms_type,
+        resolution=N,
+        L=L,
+        unitcell_frequency=unitcell_frequency,
+        invert=invert,
+        mode="shell",
+        threshold=threshold_opt,
+        shell_thickness=thickness_opt,
+    )
+    MS = MicrostructureImage(image=tpms.image)
+    print(f"Volume fraction of phase 0: {MS.volume_fractions[0]:.4f}")
+    print(f"Volume fraction of phase 1: {MS.volume_fractions[1]:.4f}")
+    MS.write(
+        h5_filename=h5_filename,
+        dset_name="threshold_opt/" + tpms_type + "_thresh_opt",
+        order="zyx",
+        compression_level=9,
+    )
+
+    # Write XDMF for visualization
+    write_xdmf(
+        h5_filepath=h5_filename,
+        xdmf_filepath="data/tpms_opt.xdmf",
+        microstructure_length=L[::-1],
+        time_series=False,
+        verbose=True,
+    )
diff --git a/docs/_templates/custom-class-template.rst b/docs/_templates/custom-class-template.rst
deleted file mode 100644
index f73eda5..0000000
--- a/docs/_templates/custom-class-template.rst
+++ /dev/null
@@ -1,34 +0,0 @@
-{{ fullname | escape | underline}}
-
-.. currentmodule:: {{ module }}
-
-.. autoclass:: {{ objname }}
-   :members:
-   :show-inheritance:
-   :inherited-members:
-   :special-members: __call__, __add__, __mul__
-
-   {% block methods %}
-   {% if methods %}
-   .. rubric:: {{ _('Methods') }}
-
-   .. autosummary::
-      :nosignatures:
-   {% for item in methods %}
-      {%- if not item.startswith('_') %}
-      ~{{ name }}.{{ item }}
-      {%- endif -%}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block attributes %}
-   {% if attributes %}
-   .. rubric:: {{ _('Attributes') }}
-
-   .. autosummary::
-   {% for item in attributes %}
-      ~{{ name }}.{{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
diff --git a/docs/_templates/custom-modules-template.rst b/docs/_templates/custom-modules-template.rst
deleted file mode 100644
index d066d0e..0000000
--- a/docs/_templates/custom-modules-template.rst
+++ /dev/null
@@ -1,66 +0,0 @@
-{{ fullname | escape | underline}}
-
-.. automodule:: {{ fullname }}
-
-   {% block attributes %}
-   {% if attributes %}
-   .. rubric:: Module attributes
-
-   .. autosummary::
-      :toctree:
-   {% for item in attributes %}
-      {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block functions %}
-   {% if functions %}
-   .. rubric:: {{ _('Functions') }}
-
-   .. autosummary::
-      :toctree:
-      :nosignatures:
-   {% for item in functions %}
-      {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block classes %}
-   {% if classes %}
-   .. rubric:: {{ _('Classes') }}
-
-   .. autosummary::
-      :toctree:
-      :template: custom-class-template.rst
-      :nosignatures:
-   {% for item in classes %}
-      {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block exceptions %}
-   {% if exceptions %}
-   .. rubric:: {{ _('Exceptions') }}
-
-   .. autosummary::
-      :toctree:
-   {% for item in exceptions %}
-      {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-{% block modules %}
-{% if modules %}
-.. autosummary::
-   :toctree:
-   :template: custom-module-template.rst
-   :recursive:
-{% for item in modules %}
-   {{ item }}
-{%- endfor %}
-{% endif %}
-{% endblock %}
diff --git a/docs/conf.py b/docs/conf.py
deleted file mode 100644
index 8968813..0000000
--- a/docs/conf.py
+++ /dev/null
@@ -1,85 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath(".."))
-# [print(i) for i in sys.path]
-
-# -- Project information -----------------------------------------------------
-
-project = "MSUtils"
-copyright = "2024, DAE"
-author = "DAE"
-
-
-# -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    "sphinx.ext.duration",
-    "sphinx.ext.autodoc",
-    "sphinx.ext.autosummary",
-    "sphinx.ext.napoleon",
-    "sphinx.ext.githubpages",
-    "nbsphinx",
-    "sphinx.ext.mathjax",
-]
-
-# napoleon for google-style docstrings: https://sphinxcontrib-napoleon.readthedocs.io/en/latest/
-# sphinx.ext.githubpages for creating .nojekyll file
-# sphinxcontrib.mermaid for mermaid-support: https://github.com/mgaitan/sphinxcontrib-mermaid
-
-autosummary_generate = True  # Turn on sphinx.ext.autosummary
-# moves typehints into docstring, but does not process them correctly:
-# from https://stackoverflow.com/a/66295922
-autodoc_typehints = "description"
-# Napoleon settings
-# napoleon_google_docstring = True
-napoleon_numpy_docstring = True
-napoleon_include_init_with_doc = False
-napoleon_include_private_with_doc = True
-napoleon_include_special_with_doc = True
-napoleon_use_admonition_for_examples = True
-napoleon_use_admonition_for_notes = True
-napoleon_use_admonition_for_references = True
-napoleon_use_ivar = False
-napoleon_use_param = True
-napoleon_use_rtype = True
-napoleon_preprocess_types = False
-napoleon_type_aliases = None
-napoleon_attr_annotations = True
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
-
-
-# -- Options for HTML output -------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = "pydata_sphinx_theme"
-# html_theme = 'alabaster'
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
diff --git a/docs/index.rst b/docs/index.rst
deleted file mode 100644
index f48c5ce..0000000
--- a/docs/index.rst
+++ /dev/null
@@ -1,26 +0,0 @@
-.. sema2024 documentation master file, created by
-   sphinx-quickstart on Thu May 16 11:28:24 2024.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to MSUTils's documentation!
-====================================
-
-Manage and investigate your computational experiments with Molten; a customisable workflow management tool with database integration.
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-   usage
-   module
-   test_cov
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/docs/module.rst b/docs/module.rst
deleted file mode 100644
index fdf70ea..0000000
--- a/docs/module.rst
+++ /dev/null
@@ -1,27 +0,0 @@
-API
-=======
-
-MSUtils
----------------------
-.. autosummary::
-   :toctree: generated
-   :template: custom-modules-template.rst
-   :recursive:
-
-
-   MSUtils.voronoi.main
-   MSUtils.voronoi.VoronoiGBErosion
-   MSUtils.voronoi.VoronoiImage
-   MSUtils.voronoi.VoronoiSeeds
-   MSUtils.voronoi.VoronoiTessellation
-   MSUtils.general.ComBoMicrostructureImage
-   MSUtils.general.compute_correlation_length
-   MSUtils.general.h52xdmf
-   MSUtils.general.MicrostructureImage
-   MSUtils.general.resize_image
-
-   .. MSUtils.lattices.lattice_definitions
-   .. MSUtils.lattices.lattice_image
-
-
-   .. MSUtils.voronoi
diff --git a/docs/scripts/push_docs.sh b/docs/scripts/push_docs.sh
deleted file mode 100644
index 7cdca5b..0000000
--- a/docs/scripts/push_docs.sh
+++ /dev/null
@@ -1,57 +0,0 @@
-#!/bin/bash
-
-time=$(date)
-REPO_URL="https://DAE:${GITHUB_TOKEN}@github.tik.uni-stuttgart.de/DAE/MSUtils.git"
-
-# Get commit info of main
-commit=$(git log -1 --pretty=%B)
-commit_sha=$(git log -1 --pretty=%H)
-commit_link="[\`$commit_sha\`](https://github.tik.uni-stuttgart.de/DAE/MSUtils/commit/$commit_sha)"
-
-# Set up gh-pages directory
-mkdir -p temp_gh_pages
-cd temp_gh_pages || { printf "Failed to enter temp_gh_pages directory\n" >&2; exit 1; }
-git clone "$REPO_URL" . || { printf "Failed to clone repository\n" >&2; exit 1; }
-git switch gh-pages || { printf "Failed to switch to gh-pages branch\n" >&2; exit 1; }
-cd .. || { printf "Failed to return to parent directory\n" >&2; exit 1; }
-
-# Copying files - docs have been created before!
-printf "Copying files...\n"
-cp -r docs/_build/html/* temp_gh_pages/ || { printf "Failed to copy files\n" >&2; exit 1; }
-
-# Add README
-printf "Add README\n"
-readmetext="# Documentation Branch
-
-This Branch is only meant to host the documentation via github-pages. Nothing to see here. The contents of this branch are essentially a cache that's not intended to be viewed on github.com.
-
-You can find it [here](https://pages.github.tik.uni-stuttgart.de/DAE/MSUtils/).
-
-**It is not to be merged with main!**
-
-For the actual repository, go to branch \`main\`.
-
-## Current State reflected:
-
-### Last update: $time
-
-### Commit SHA:
-$commit_link
-
-### Title:
-$commit
-"
-
-cd temp_gh_pages || { printf "Failed to enter temp_gh_pages directory\n" >&2; exit 1; }
-printf "%s" "$readmetext" > README.md || { printf "Failed to write README.md\n" >&2; exit 1; }
-git add -A || { printf "Failed to add files to git\n" >&2; exit 1; }
-git commit -m "Deploy for commit '$commit_sha', '$commit' on $time" || { printf "Failed to commit changes\n" >&2; exit 1; }
-
-# Pushing files
-printf "Pushing files\n"
-printf "%s\n" "$commit"
-git push --force-with-lease origin gh-pages || { printf "Failed to push changes\n" >&2; exit 1; }
-
-# Cleanup
-cd .. || { printf "Failed to return to parent directory\n" >&2; exit 1; }
-rm -rf temp_gh_pages || { printf "Failed to remove temp_gh_pages directory\n" >&2; exit 1; }
diff --git a/docs/scripts/update_docs_by_hand.ps1 b/docs/scripts/update_docs_by_hand.ps1
deleted file mode 100644
index 26d1339..0000000
--- a/docs/scripts/update_docs_by_hand.ps1
+++ /dev/null
@@ -1,45 +0,0 @@
-$time = Get-Date
-# Set up gh-pages directory
-mkdir temp_gh_pages
-Set-Location temp_gh_pages
-git clone https://github.tik.uni-stuttgart.de/DAE/MSUtils.git .
-git switch gh-pages
-Set-Location ..
-# Make New main directory
-mkdir temp_main
-Set-Location temp_main
-git clone https://github.tik.uni-stuttgart.de/DAE/MSUtils.git .
-$commit = git log -1 --pretty=%B
-# Build new website
-# pixi run -v test # Does not work, don't know why... covhtml does not get copied
-pixi run -v -e utility sphinx-build -M html docs docs/_build
-Write-Output "compiling done!"
-# Copying
-Write-Output "Copying files..."
-Copy-Item -r -force -v docs/_build/html/* ../temp_gh_pages/
-Write-Output "Add README"
-$readmetext = "# Documentation Branch
-
-This Branch is only meant to host the documentation via github-pages. Nothing to see here. The contents of this branch are essentially a cache that's not intended to be viewed on github.com.
-
-You can find it [here](https://pages.github.tik.uni-stuttgart.de/DAE/MSUtils/).
-
-**It is not to be merged with main!**
-
-For the actual repository, go to branch `main`.
-
-## Current State reflected:
-$commit
-"
-Set-Location ../temp_gh_pages
-New-Item -Path README.md -Force
-$readmetext | Add-Content -Path .\README.md
-git add -A
-git commit -a -m "Deploy for commit '$commit' on $time"
-Write-Output "Pushing files"
-Write-Output $commit
-git push --force-with-lease origin gh-pages
-
-Set-Location ..
-Remove-Item .\temp_gh_pages\ -r -Force
-Remove-Item .\temp_main\ -r -Force
diff --git a/docs/scripts/update_docs_by_hand.sh b/docs/scripts/update_docs_by_hand.sh
deleted file mode 100644
index 2a3ecb6..0000000
--- a/docs/scripts/update_docs_by_hand.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/bash
-
-time=$(date)
-REPO_URL="https://github.tik.uni-stuttgart.de/DAE/MSUtils.git"
-
-# Set up gh-pages directory
-mkdir -p temp_gh_pages
-cd temp_gh_pages || { printf "Failed to enter temp_gh_pages directory\n" >&2; exit 1; }
-git clone "$REPO_URL" . || { printf "Failed to clone repository\n" >&2; exit 1; }
-git switch gh-pages || { printf "Failed to switch to gh-pages branch\n" >&2; exit 1; }
-cd .. || { printf "Failed to return to parent directory\n" >&2; exit 1; }
-
-# Make New main directory
-mkdir -p temp_main
-cd temp_main || { printf "Failed to enter temp_main directory\n" >&2; exit 1; }
-git clone "$REPO_URL" . || { printf "Failed to clone repository\n" >&2; exit 1; }
-commit=$(git log -1 --pretty=%B)
-cd .. || { printf "Failed to return to parent directory\n" >&2; exit 1; }
-
-# Build new website
-# pixi run test # Does not work, don't know why... covhtml does not get copied
-pixi run -v -e docs sphinx-build -M html docs docs/_build || { printf "Failed to build documentation\n" >&2; exit 1; }
-printf "Compiling done!\n"
-
-# Copying files
-printf "Copying files...\n"
-cp -r docs/_build/html/* temp_gh_pages/ || { printf "Failed to copy files\n" >&2; exit 1; }
-
-# Add README
-printf "Add README\n"
-readmetext="# Documentation Branch
-
-This Branch is only meant to host the documentation via github-pages. Nothing to see here. The contents of this branch are essentially a cache that's not intended to be viewed on github.com.
-
-You can find it [here](https://pages.github.tik.uni-stuttgart.de/DAE/MSUtils/).
-
-**It is not to be merged with main!**
-
-For the actual repository, go to branch \`main\`.
-
-## Current State reflected:
-$commit
-"
-
-cd temp_gh_pages || { printf "Failed to enter temp_gh_pages directory\n" >&2; exit 1; }
-printf "%s" "$readmetext" > README.md || { printf "Failed to write README.md\n" >&2; exit 1; }
-git add -A || { printf "Failed to add files to git\n" >&2; exit 1; }
-git commit -m "Deploy for commit '$commit' on $time" || { printf "Failed to commit changes\n" >&2; exit 1; }
-
-# Pushing files
-printf "Pushing files\n"
-printf "%s\n" "$commit"
-git push --force-with-lease origin gh-pages || { printf "Failed to push changes\n" >&2; exit 1; }
-
-# Cleanup
-cd .. || { printf "Failed to return to parent directory\n" >&2; exit 1; }
-rm -rf temp_gh_pages || { printf "Failed to remove temp_gh_pages directory\n" >&2; exit 1; }
-rm -rf temp_main || { printf "Failed to remove temp_main directory\n" >&2; exit 1; }
diff --git a/docs/test_cov.rst b/docs/test_cov.rst
deleted file mode 100644
index 03ddeab..0000000
--- a/docs/test_cov.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-Test Coverage
-=============
-
-This page leads now to the test-coverage webpage.
-There is no way back! Open it as a new tab...
-
-`Coverage Report <_static/test_cov/index.html>`_
diff --git a/docs/usage.rst b/docs/usage.rst
deleted file mode 100644
index 3527365..0000000
--- a/docs/usage.rst
+++ /dev/null
@@ -1,27 +0,0 @@
-Usage
-=====
-
-Installation
-------------
-
-To use MSUtils one can use different methods of installing.
-
-Installation via pip and the github-repo:
-
-.. code-block:: console
-
-   (.venv) $ pip install git+https://github.tik.uni-stuttgart.de/DAE/molten
-
-
-Development
-------------
-
-One can create a pip or conda environment using the dependencies described in the pyproject.toml .
-To use the pixi environment and workflow-manager, just install pixi from `here
-<https://pixi.sh/latest/>`_ . After that, navigate to the cloned environment and execute
-
-.. code-block:: console
-
-    pixi install
-
-After this install, the pixi environment can be used in all major IDEs etc.
diff --git a/pixi.lock b/pixi.lock
index 7c6a05b..c7fe374 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -16,8 +16,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.2-h39aace5_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.3.0-pyh71513ae_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/beartype-0.21.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyh71513ae_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/beartype-0.22.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hb03c661_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hb03c661_4.conda
@@ -26,11 +26,11 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.21.3-h4cfbee9_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2025.8.3-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2025.10.5-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py311h5b438cf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cfgv-3.3.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/charls-2.4.2-h59595ed_0.conda
@@ -61,11 +61,11 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.60.0-py311h3778330_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.60.1-py311h3778330_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.16-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/frozenlist-1.7.0-py311h52bc045_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.44.2-h2b0a6b4_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.44.3-h2b0a6b4_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gettext-0.25.1-h3f43e3d_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.25.1-h3f43e3d_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda
@@ -80,13 +80,13 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.24.11-hc37bda9_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/h5py-3.14.0-nompi_py311h0b2f468_101.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-11.5.1-h15599e2_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-12.1.0-h15599e2_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf4-4.2.15-h2a13503_7.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.14.6-nompi_h6e4c0c1_103.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/identify-2.6.14-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/identify-2.6.15-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.10-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/imagecodecs-2025.8.2-py311h5031496_4.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/imageio-2.37.0-pyhfb79c49_0.conda
@@ -94,7 +94,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/intel-gmmlib-22.8.2-hb700be7_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/intel-media-driver-25.3.4-hecca717_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.30.1-pyh82676e8_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/ipython-9.5.0-pyhfa0c392_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/ipython-9.6.0-pyhfa0c392_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ipython_pygments_lexers-1.1.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jedi-0.19.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/jsoncpp-1.9.6-hf42df4d_1.conda
@@ -107,7 +107,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/lame-3.100-h166bdaf_1003.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/lazy-loader-0.4-pyhd8ed1ab_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/level-zero-1.24.3-hb700be7_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libabseil-20250512.1-cxx17_hba17884_0.conda
@@ -125,7 +125,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hb03c661_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcap-2.76-h0b2e76d_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-20_linux64_openblas.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libclang-cpp20.1-20.1.8-default_h99862b1_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libclang-cpp20.1-20.1.8-default_h99862b1_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libclang-cpp21.1-21.1.0-default_h99862b1_1.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-hb8b1518_5.conda
@@ -141,14 +141,14 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libflac-1.4.3-h59595ed_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.1-h73754d4_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-h767d61c_6.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_6.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcrypt-lib-1.11.1-hb9d3cd8_0.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-devel-0.25.1-h3f43e3d_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-15.1.0-h69a702a_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_6.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-15.2.0-h69a702a_6.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-hcd61629_6.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgl-1.7.0-ha4b6fd6_2.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-64/libglib-2.86.0-h1fed272_0.conda
@@ -156,10 +156,10 @@ environments:
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_6.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.12.1-default_h3d81e11_1000.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libhwy-1.3.0-h4c17acf_0.conda
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   md5: 17dcc85db3c7886650b8908b183d6876
diff --git a/pyproject.toml b/pyproject.toml
index 017baf7..0309768 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,11 +33,11 @@ scipy = ">=1.11.4,<2"
 matplotlib = ">=3.10.6,<4"
 scikit-image = ">=0.25.2,<0.26"
 lxml = ">=6.0.2,<7"
-plotly = ">=6.3.0,<7"
+plotly = ">=6.3.1,<7"
 sympy = ">=1.14.0,<2"
 ipykernel = ">=6.30.1,<7"
 quaternion = ">=2024.0.12,<2025"
-beartype = ">=0.21.0,<0.22"
+beartype = ">=0.22.2,<0.23"
 pre-commit = ">=4.3.0,<5"
 puma = ">=3.2.0,<4"
 pyvista = ">=0.46.3,<0.47"
diff --git a/test/test_MicrostructureImage.py b/test/test_MicrostructureImage.py
deleted file mode 100644
index 9594846..0000000
--- a/test/test_MicrostructureImage.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from MSUtils.general.MicrostructureImage import main as MicrostructureImage_main
-
-
-def test_MicrostrutureImage():
-    MicrostructureImage_main()
diff --git a/test/test_VoronoiSeeds.py b/test/test_VoronoiSeeds.py
deleted file mode 100644
index 8437c5c..0000000
--- a/test/test_VoronoiSeeds.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from MSUtils.voronoi.VoronoiSeeds import main as VoronoiSeeds_main
-
-
-def test_VoronoiSeeds():
-    VoronoiSeeds_main()
diff --git a/test/test_main.py b/test/test_main.py
deleted file mode 100644
index 978dd1d..0000000
--- a/test/test_main.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from MSUtils.voronoi.main import main as voronoi_main
-
-
-def test_voronoi_main():
-    voronoi_main()
diff --git a/test/test_resize_image.py b/test/test_resize_image.py
deleted file mode 100644
index 8697148..0000000
--- a/test/test_resize_image.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from MSUtils.general.resize_image import main as resize_image_main
-
-
-def test_resize_image():
-    resize_image_main()