added more docs

docs/howto.md

@@ -0,0 +1,20 @@
+
+
+Microscopic images usually come with a large stack: many high-resolution slices!
+
+There are two ways to utilize this plugin over a large stack:
+
+- **One Model for All**: Training an RF model on a small sub-stack, then predicting over the entire stack.
+- **Divide And Conquer**: Dividing the large stack into several sub-stacks, then train an RF model for each.
+
+## One Model For All
+As for the first step, we recommend making a small sub-stack to train a Random Forest (RF) model using our plugin. This sub-stack can have about 20 slices selected across the whole stack (not just the beginning or last few slices). This way, when you extract and save the sub-stack's features, the storage file won't occupy too much space on the hard drive.  
+
+!!! tip
+    If the image resolution is high, it's better to down-scale the images into a resolution of below 1200 pixels for the largest dimension.
+
+After the training, you can save the RF model, and later apply it on the entire stack.  
+
+## Divide And Conquer
+Extracted features saved as an `HDF5` file can take a very large space on disk. In this method, to prevent the disk space overflow, you can divide your large stack into several sub-stacks. Then use the plugin for each, separately.  
+Although, you can try one trained model over another sub-stack, Random Forest model can not be fine-tuned. By using this method, you can achieve better annotations with the expense of spending more time on training several models.

docs/index.md

@@ -4,12 +4,21 @@ title: Welcome
 
 # Welcome to Feature Forest Documentation
 
-Feature Forest (**FF**) is a *[napari]* plugin for creating image annotations with less manual work, utilizing image embeddings (*features*) of vision transformer models like *[SAM2]* and training a *Random Forest* model using a little scribble labels provided by the user.
+Feature Forest (**FF**) is a [napari] plugin for creating image annotations with less manual work, utilizing image embeddings (*features*) of vision transformer models like [SAM2], and training a *Random Forest* model using a little scribble labels provided by the user.
 
 ### Overview
-![figure 1](assets/fig1.png)
+FF plugin includes two widgets: **Feature Extractor** and **Segmentation** widgets.
 
+![Feature Extractor](assets/extractor_1.png){width="300"}
+/// caption
+Feature Extractor Widget
+///
 
+![Feature Extractor](assets/segmentation_1.png){width="300" align=left}
+![Feature Extractor](assets/segmentation_2.png){width="300" align=right}
+/// caption
+Segmentation Widget
+///
 
 
 [napari]: https://napari.org/

docs/install.md

@@ -1,7 +1,3 @@
----
-title: Installation
----
-
 ## Easy Way!
 To install this plugin you need to use [mamba] or [conda] to create a environment and install the requirements. Use the commands below to create the environment and install the plugin:
 ```bash
@@ -50,6 +46,11 @@ cd ./featureforest
 pip install .
 ```
 
-[PyPI]: https://pypi.org/
+There is also a [pypi package](https://pypi.org/project/featureforest/) available that you can install using `pip`:
+```bash
+pip install featureforest
+```
+
+
 [conda]: https://conda.io/projects/conda/en/latest/index.html
 [mamba]: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html

docs/stylesheets/extra.css

@@ -1,4 +1,13 @@
 .md-typeset code {
-    font-size: 90%;
+    font-size: 91%;
     font-weight: 600;
+}
+
+/* Maximum space for text block */
+.md-grid {
+    max-width: 71rem;
+}
+
+.admonition>:last-child, html .md-typeset details>:last-child {
+    font-size: 0.72rem;
 }

mkdocs.yml

@@ -1,15 +1,9 @@
-site_name: Feature Forest Documents
+site_name: Feature Forest Documentation
 site_url: https://juglab.github.io/featureforest
 extra_css:
   - stylesheets/extra.css
 theme:
   name: material
-  features:
-    - navigation.footer
-    - navigation.sections
-    - navigation.instant
-    - navigation.instant.progress
-    - content.code.copy
   # logo: assets/logo.png
   # favicon: images/favicon.png
   icon:
@@ -34,6 +28,21 @@ theme:
         icon: material/brightness-7 
         name: Switch to dark mode
 
+  features:
+    - navigation.footer
+    - navigation.indexes
+    - navigation.sections
+    - navigation.instant
+    - navigation.instant.progress
+    - navigation.path
+    - navigation.top
+    - content.code.copy
+
+nav:
+  - Welcome: index.md
+  - Installation: install.md
+  - How to use the plugin: howto.md
+
 extra:
   version:
       provider: mike
@@ -49,6 +58,14 @@ markdown_extensions:
       anchor_linenums: true
       line_spans: __span
       pygments_lang_class: true
+  - admonition
+  - attr_list
+  - md_in_html
   - pymdownx.inlinehilite
   - pymdownx.snippets
-  - pymdownx.superfences
+  - pymdownx.superfences
+  - pymdownx.details
+  - pymdownx.blocks.caption
+  - def_list
+  - pymdownx.tasklist:
+      custom_checkbox: true