diff --git a/docs/assets/qim3d-icon.svg b/docs/assets/qim3d-icon.svg
new file mode 100644
index 0000000000000000000000000000000000000000..912830615e043ba24dc9aef18ed76e24ea229b00
--- /dev/null
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diff --git a/docs/gui.md b/docs/gui.md
new file mode 100644
index 0000000000000000000000000000000000000000..40e99eca9873ede206118aaa89b54b865b105c7f
--- /dev/null
+++ b/docs/gui.md
@@ -0,0 +1,3 @@
+::: qim3d.gui.data_explorer
+::: qim3d.gui.iso3d
+::: qim3d.gui.local_thickness
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000000000000000000000000000000000000..b2d702e3d08455ebd386fda62a075afc36d9ccfd
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,76 @@
+# <img src="assets/qim3d-logo.png" width="300px">
+
+
+`qim3d` is a Python library for quantitative imaging analysis in 3D. It provides functionality for handling data, as well as tools for visualization and analysis.
+
+
+## Installation
+
+Install the latest stable version by using pip:
+
+```
+pip install qim3d
+```
+
+
+## Getting started
+
+Some basic funtionalites are descibred here. The full documentation is still under development.
+
+### Loading Data
+To load image data from a file, use `qim.io.load()`
+
+```python
+import qim3d
+
+# Load a file
+vol = qim3d.io.load("path/to/file.tif")
+
+# Load a file as a virtual stack
+vol = qim3d.io.load("path/to/file.tif", virtual_stack=True)
+```
+
+### Visualize data
+You can easily check slices from your volume using `slice_viz`
+
+```python
+import qim3d
+
+img = qim3d.examples.fly_150x256x256
+
+# By default shows the middle slice
+qim3d.viz.slice_viz(img)
+
+# Or we can specifly positions
+qim3d.viz.slice_viz(img, position=[0,32,128])
+
+# Parameters for size and colormap are also possible
+qim3d.viz.slice_viz(img, img_width=6, img_height=6, cmap="inferno")
+
+```
+
+
+### GUI Components
+The library also provides GUI components for interactive data analysis and exploration.
+The `qim3d.gui` module contains various classes for visualization and analysis:
+
+```python
+import qim3d
+
+app = qim3d.gui.iso3d.Interface()
+app.launch()
+```
+
+GUIs can also be launched using the Qim3D CLI:
+```
+$ qim3d gui --data-explorer
+```
+
+## Contributing
+Contributions to `qim3d` are welcome! If you find a bug, have a feature request, or would like to contribute code, please open an issue or submit a pull request.
+
+You can find us at Gitlab:
+https://lab.compute.dtu.dk/QIM/tools/qim3d
+
+## License
+This project is licensed under the MIT License.
\ No newline at end of file
diff --git a/docs/io.md b/docs/io.md
new file mode 100644
index 0000000000000000000000000000000000000000..f72aa9b9a542079fa5c2629fbd26cc6de6567f6d
--- /dev/null
+++ b/docs/io.md
@@ -0,0 +1,3 @@
+::: qim3d.io.load
+::: qim3d.io.save
+::: qim3d.io.downloader
\ No newline at end of file
diff --git a/docs/models.md b/docs/models.md
new file mode 100644
index 0000000000000000000000000000000000000000..079b974aa54d15e14ab5b3cdfed63f62239b6ed6
--- /dev/null
+++ b/docs/models.md
@@ -0,0 +1 @@
+::: qim3d.models.unet
\ No newline at end of file
diff --git a/docs/releases.md b/docs/releases.md
new file mode 100644
index 0000000000000000000000000000000000000000..5a72d14cf5d802621c9b634a700a9a874ce18caf
--- /dev/null
+++ b/docs/releases.md
@@ -0,0 +1,50 @@
+# Release history
+Here you can fin details about the version history of `qim3d`
+
+## v0.3.1 (February 1, 2024)
+
+- Save functionality for all file formats
+
+### Just for tests
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
+
+
+
+## v0.3.0 (January 23, 2024)
+
+- Introduction of qim3d CLI
+- Data Explorer GUI
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
+
+
+## v0.2.0 (Sept 18, 2023)
+
+Includes new develoments toward the usability of the library, as well as its integration with the QIM platform.
+
+- Refactored code for the graphical interfaces
+ - For the local thicknes GUI, now it is possible to pass and receive numpy arrays instead of using the upload functionality.
+- Improved data loader
+ - Now the extensions `tif`, `h5` and `txm` are supported.
+- Added `qim3d.viz.slice_viz` for easy slice visualization.
+- U-net model creation
+ - Model availabe from `qim3d.models.UNet`
+ - Data augmentation class at `qim3d.utils.Augmentation`
+ - Notebook with full pipeline at `docs/notebooks/Unet.ipynb`
+- Image examples accessible from `qim3d.examples`
+
+
+## v0.1.3 (May 17, 2023)
+
+First stable release.
+
+- Simple Tiff data loader
+- Graphical interfaces
+ - Local thickness
+ - 3D Isosurfaces
+ - Data exploration tool
\ No newline at end of file
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
new file mode 100644
index 0000000000000000000000000000000000000000..4b12b898e2cf7d12718daa1b032742c37e7f923b
--- /dev/null
+++ b/docs/stylesheets/extra.css
@@ -0,0 +1,44 @@
+.md-search__form{
+ border-radius: 8px;
+}
+
+.md-search__form:hover{
+ background-color: #f0f0f0 !important;
+}
+
+.md-search__inner{
+ border-radius: 0px !important;
+}
+
+.md-nav__item .md-nav__link--active, .md-nav__item .md-nav__link--active code {
+ color: orange}
+
+.md-typeset a {
+ color: orange;
+ word-break: break-word;
+}
+
+.md-nav__link {
+ font-size: 1.0em;
+}
+
+.md-nav:first-child {
+ font-size: 2.0em;
+}
+
+code {
+ border-radius: 6px !important;
+}
+
+.md-tabs__list li:last-child {
+ margin-left: auto;
+}
+
+
+.md-header__source {
+ text-align: right;
+}
+
+.md-header__title {
+ margin-left: 0px !important;
+}
\ No newline at end of file
diff --git a/docs/utils.md b/docs/utils.md
new file mode 100644
index 0000000000000000000000000000000000000000..a1b939cea4e1cdb36138bd3ef2604106d81bdda9
--- /dev/null
+++ b/docs/utils.md
@@ -0,0 +1,4 @@
+::: qim3d.utils.system
+ options:
+ members:
+ - Memory
\ No newline at end of file
diff --git a/docs/version_history.md b/docs/version_history.md
deleted file mode 100644
index 26318aa2b9454e55a32d807d1d7bc666528a2c89..0000000000000000000000000000000000000000
--- a/docs/version_history.md
+++ /dev/null
@@ -1,31 +0,0 @@
-# Release history
-Here you can fin details about the version history of `qim3d`
-
-
-## v0.2.0 (Sept 18, 2023)
-```pip install qim3d==0.2.0```
-
-Includes new develoments toward the usability of the library, as well as its integration with the QIM platform.
-
-- Refactored code for the graphical interfaces
- - For the local thicknes GUI, now it is possible to pass and receive numpy arrays instead of using the upload functionality.
-- Improved data loader
- - Now the extensions `tif`, `h5` and `txm` are supported.
-- Added `qim3d.viz.slice_viz` for easy slice visualization.
-- U-net model creation
- - Model availabe from `qim3d.models.UNet`
- - Data augmentation class at `qim3d.utils.Augmentation`
- - Notebook with full pipeline at `docs/notebooks/Unet.ipynb`
-- Image examples accessible from `qim3d.examples`
-
-
-## v0.1.3 (May 17, 2023)
-```pip install qim3d==0.1.3```
-
-First stable release.
-
-- Simple Tiff data loader
-- Graphical interfaces
- - Local thickness
- - 3D Isosurfaces
- - Data exploration tool
\ No newline at end of file
diff --git a/docs/viz.md b/docs/viz.md
new file mode 100644
index 0000000000000000000000000000000000000000..5a92ef563318870fc96d5ed39a2355fbec666f27
--- /dev/null
+++ b/docs/viz.md
@@ -0,0 +1,18 @@
+# Data visualization
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
+
+Example:
+```python
+import qim3d
+```
+
+
+::: qim3d.viz.img
+ options:
+ members:
+ - grid_overview
+ - grid_pred
+ - slice_viz
+
+
+
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000000000000000000000000000000000000..ef07ca04fa6b6d77eb2285958a741d0c83d69d43
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,66 @@
+site_name: qim3d documentation
+site_url: https://platform.qim.dk/qim3d/
+site_author: Qim3d contributors
+site_description: Documentation for the Qim3d python library
+repo_url: https://lab.compute.dtu.dk/QIM/tools/qim3d
+repo_name: Source code at Gitlab
+
+
+nav:
+ - 📦 qim3d: index.md
+ - 📥 Input & Output: io.md
+ - 📊 Visualization: viz.md
+ - 🔧 Utils: utils.md
+ - 🖥️ GUIs: gui.md
+ - 🧠 ML Models: models.md
+ - 📋 Release history: releases.md
+
+theme:
+ language: en
+ name: material
+ nav_position: top
+ logo: assets/qim3d-icon.svg
+ favicon: assets/qim3d-icon.svg
+ features:
+ - navigation.tabs
+ # - navigation.expand
+ # - navigation.instant
+ - toc.integrate
+ - toc.follow
+ - search.suggest
+ # - content.tabs.link
+ # - content.code.annotation
+ - content.code.copy
+
+ palette:
+ primary: white
+ accent: orange
+
+
+extra_css:
+ - stylesheets/extra.css
+
+extra:
+ social:
+ - icon: fontawesome/brands/x-twitter
+ link: https://twitter.com/QIMCenter
+
+markdown_extensions:
+ - pymdownx.highlight:
+ anchor_linenums: true
+ - pymdownx.superfences
+
+plugins:
+ - tags
+ - search
+ - mkdocstrings:
+ handlers:
+ python:
+ options:
+ show_root_heading: true
+ show_source: true
+ show_root_full_path: true
+ show_object_full_path: true
+ show_symbol_type_heading: true
+ show_symbol_type_toc: true
+ separate_signature: true
\ No newline at end of file
diff --git a/qim3d/io/load.py b/qim3d/io/load.py
index f6b118484de9e289267f277bda487c271a38e49e..a761d3283ba7b87774210d82a1c6a29de4537827 100644
--- a/qim3d/io/load.py
+++ b/qim3d/io/load.py
@@ -1,4 +1,14 @@
-"""Provides functionality for loading data from various file formats."""
+"""
+Provides functionality for loading data from various file formats.
+
+
+Example:
+ ```
+ import qim3d
+ data = qim3d.io.load("image.tif")
+ ```
+
+"""
import difflib
import os
diff --git a/qim3d/viz/img.py b/qim3d/viz/img.py
index e3648f5445c7a4449c2b42057c78b2db9e48e381..804cdd289d3060f72502e0cd3fb0c8ae05b40450 100644
--- a/qim3d/viz/img.py
+++ b/qim3d/viz/img.py
@@ -1,4 +1,6 @@
-""" Provides a collection of visualization functions."""
+"""
+Provides a collection of visualization functions.
+"""
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap
from matplotlib import colormaps
@@ -25,18 +27,21 @@ def grid_overview(data, num_images=7, cmap_im="gray", cmap_segm="viridis", alpha
Raises:
ValueError: If the data elements are not tuples.
- Notes:
- - If the image data is RGB, the color map is ignored and the user is informed.
- - The number of displayed images is limited to the minimum between `num_images`
- and the length of the data.
- - The grid layout and dimensions vary based on the presence of a mask.
Returns:
fig (matplotlib.figure.Figure): The figure with an overview of the images and their labels.
Example:
+ ```python
data = [(image1, label1, mask1), (image2, label2, mask2)]
grid_overview(data, num_images=5, cmap_im='viridis', cmap_segm='hot', alpha=0.8)
+ ```
+
+ Notes:
+ - If the image data is RGB, the color map is ignored and the user is informed.
+ - The number of displayed images is limited to the minimum between `num_images`
+ and the length of the data.
+ - The grid layout and dimensions vary based on the presence of a mask.
"""
# Check if data has a mask