Updated docs

docs/code_example.md

@@ -7,7 +7,7 @@ These code snippets walk you through a small stitching workflow consisting of
   3. Stitching / fusing the tiles
 
 
-### 1) Prepare data for stitching
+#### 1) Prepare data for stitching
 
 
 ```python
@@ -48,7 +48,7 @@ for tile_array, tile_translation in zip(tile_arrays, tile_translations):
 
 ![Visualization of input tile configuration](images/tile_configuration.png)
 
-### 2) Register the tiles
+#### 2) Register the tiles
 
 ```python
 from dask.diagnostics import ProgressBar
@@ -66,7 +66,7 @@ with ProgressBar():
 # vis_utils.plot_positions(msims, transform_key='translation_registered', use_positional_colors=False)
 ```
 
-### 3) Stitch / fuse the tiles
+#### 3) Stitch / fuse the tiles
 ```python
 from multiview_stitcher import fusion
 

docs/index.md

@@ -1,4 +1,8 @@
-# Overview
+---
+title: Overview
+---
+
+# multiview-stitcher
 
 [`multiview-stitcher`](https://github.com/multiview-stitcher/multiview-stitcher) is an open-source modular toolbox for distributed and tiled stitching of 2-3D image data in python. It is an extensible framework including a collection of algorithms to **register** and **fuse** small and large datasets from **multi-positioning** and **multi-view** light sheet microscopy, as well as **other modalities** such as correlative cryo-EM datasets.
 
@@ -9,12 +13,12 @@ With a focus on interoperability and integration with existing tools and the eco
 It leverages [`xarray`](https://github.com/xarray) in combination with [`spatial-image`](https://github.com/spatial-data) classes for image metadata handling and [`dask`](https://github.com/dask) (and [`dask-image`](https://github.com/dask-image)) for chunked and distributed image processing.
 
 
-### Napari plugin
+## Napari plugin
 
 There's an associated napari plugin: [napari-stitcher](https://github.com/multiview-stitcher/napari-stitcher).
 
 
-### Previous work
+## Previous work
 
 `multiview-stitcher` improves and replaces [MVRegFus](https://github.com/m-albert/MVRegFus).
 

mkdocs.yml

@@ -70,24 +70,26 @@ theme:
     - navigation.footer  # next/previous links in footer
     - navigation.instant
     - navigation.instant.progress
+  logo: images/logo.png
   icon:
-    logo: fontawesome/solid/clone
+    # logo: fontawesome/solid/clone
+
     repo: fontawesome/brands/github
   favicon:
   palette:
     # Palette toggle for light mode
     - media: "(prefers-color-scheme: light)"
       scheme: default
-      primary: dark blue
+      primary: white
       accent: dark blue
       toggle:
         icon: material/lightbulb-outline
         name: Switch to dark mode
     # Palette toggle for dark mode
     - media: "(prefers-color-scheme: dark)"
       scheme: slate
-      primary: teal
-      accent: light green
+      primary: grey
+      accent: light blue
       toggle:
         icon: material/lightbulb
         name: Switch to light mode