Merge pull request #42 from mapmanager/tmp-branch

Tmp branch

docs/about.md

@@ -1,3 +1,3 @@
-The brightest-path-tracing Python package was developed by Vasudha Jha as a Computer Science Masters project in the [lab of Robert Cudmore](https://cudmorelab.github.io/) at the University of California at Davis.
+The brightest-path-tracing Python package was developed by [Vasudha Jha](https://github.com/VasudhaJha) as a Computer Science Masters project in collaboration with [Robert Cudmore](https://github.com/cudmore) in the [Cudmore lab](https://cudmorelab.github.io/) at the University of California at Davis.
 
 Please get in touch if you would like to use any of our tools.

docs/index.md

@@ -1,11 +1,34 @@
-# Overview
-
 The `brightest-path-lib` is a Python library which allows users to efficiently find the path with the maximum brightness in a 2D or 3D images. It uses the A\* Search and NBA\* Search algorithms, which are informed search algorithms that use heuristics to guide the search towards the most promising areas of the image.
 
+<!-- <figure markdown>
+  ![Finding Brightest Path using A* Search](./assets/astar.gif)
+  <figcaption>Finding Brightest Path using A* Search</figcaption>
+</figure>
+<figure markdown>
+  ![Finding Brightest Path using NBA* Search](./assets/nbastar.gif)
+  <figcaption>Finding Brightest Path using NBA* Search</figcaption>
+</figure> -->
+
+## Examples
+
+In these examples, a search is performed from the user specified start (green) and stop (red) points. The progress of the search is animated as cyan fill color and the final brightest-path is shown in yellow.
+
+Finding Brightest Path using A* Search
+![Finding Brightest Path using A* Search](./assets/images/astar-v2.gif)
+
+Finding Brightest Path using NBA* Search
+![Finding Brightest Path using NBA* Search](./assets/images/nbastar-v2.gif)
+
 ## Capabilities
 
+With its efficient implementation and intuitive API, this library is a valuable tool for anyone working with 2D or 3D images who needs to identify the path with the maximum brightness.
+
 - The library provides easy-to-use functions that take the image data and start and end points as input and return the path with the maximum brightness as output.
 - It supports both grayscale and color images and can handle images of arbitrary sizes.
 - The library also provides support for users to know which points in the image are being considered for the brightest path in real-time so that they display them on the original image.
 
-With its efficient implementation and intuitive API, this library is a valuable tool for anyone working with 2D or 3D images who needs to identify the path with the maximum brightness. We are using it for neuronal tracing to identify the path of a neuron or a set of neurons through a stack of images in our Napari Plugin.
+## Napi Plugin
+
+We have also created a [Napari Tracing Plugin](https://github.com/mapmanager/napari-tracing) to provide an intuititive graphical-user-interface that uses the `brightest-path-lib`` package. We are using this to trace neuronal dendrites and axons.
+
+![Napari Tracing Plugin](./assets/images/tracing-plugin.png)

docs/overview.md

@@ -1,38 +1,3 @@
-<style>
-#videotable {
-    /*float: right;*/
-    border: 0px solid #ddd;
-    padding: 5px;
-    /* font-family: "Trebuchet MS", Arial, Helvetica, sans-serif; */
-    /* border-collapse: collapse; */
-    /* width: 100%; */
-}
-
-#videotable td, #videotable th {
-    border: 0px solid #ddd;
-    text-align: left;
-    valign: top
-    padding: 5px;
-    /* padding: 8px; */
-}
-
-#videotable tr:nth-child(even){
-	/* background-color: #f2f2f2; */
-}
-
-/* #videotable tr:hover {background-color: #ddd;} */
-
-#videotable th {
-    /* padding-top: 12px; */
-    /* padding-bottom: 12px; */
-    text-align: left;
-    background-color: #4CAF50;
-    color: white;
-}
-</style>
-
-# Overview
-
 The `brightest-path-lib` is a Python library which allows users to efficiently find the path with the maximum brightness in a 2D or 3D images. It uses the A\* Search and NBA\* Search algorithms, which are informed search algorithms that use heuristics to guide the search towards the most promising areas of the image.
 
 <!-- <figure markdown>

mkdocs.yml

@@ -1,5 +1,11 @@
 # mkdocs.yml
 site_name: Brightest Path Library
+site_description: A library of path-finding algorithms to find the brightest path between two points.
+site_author: Robert H Cudmore
+
+repo_name: brightest-path-lib
+repo_url: https://github.com/mapmanager/brightest-path-lib
+edit_uri: ""
 
 theme:
   name: "material"
@@ -23,7 +29,7 @@ markdown_extensions:
   - md_in_html
 
 nav:
-  - Overview: overview.md
+  - Introduction: index.md
   - Getting Started:
     - installation.md
     - quickstart_guide.md