app docs (#360)

Author: ksikka

docs/_static/lightningpose.css

@@ -1,3 +1,8 @@
+/* Hide the main title only on the homepage */
+.home-display-none h1:first-child {
+    display: none;
+}
+
 /*
     Hacks to fix sphinx-rtd-theme styles leaking past dark theme
     Related issue: https://github.com/MrDogeBro/sphinx_rtd_dark_mode/issues/43

docs/index.rst

@@ -1,45 +1,212 @@
-.. lightning-pose documentation master file, created by
-   sphinx-quickstart on Thu Nov  9 13:15:31 2023.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+.. rst-class:: home-display-none
+
+Lightning Pose Homepage
+========================
 
 .. image:: images/LightningPose_horizontal_light.png
 
-Welcome to the Lightning Pose documentation
-===========================================
 
-Lightning Pose is an open source deep learning package for animal pose estimation
-(`Biderman, Whiteway et al. 2024, Nature Methods <https://rdcu.be/dLP3z>`_).
-The framework is based on Pytorch Lightning and supports accelerated training on unlabeled videos
-using NVIDIA DALI. Models can be evaluated with TensorBoard and Streamlit.
-We also offer a suite of tools for multi-camera pose estimation.
+.. meta::
+   :description: Accessible documentation for animal pose estimation.
+
+.. raw:: html
+
+    <div style="text-align: center; margin-top: 1em; margin-bottom: 2em;">
+        <p style="font-size: 1.2em;">An end-to-end toolkit for robust multi-view animal pose estimation.</p>
+    </div>
+
+.. grid:: 1 1 3 3
+    :gutter: 3
+    :class-container: feature-card-container
+
+    .. grid-item-card:: 🛰️ Multi-View
+        :class-card: feature-toggle-card
+
+        Multiview transformers and patch masking for robust 3D tracking.
+
+    .. grid-item-card:: 🎬 Single-View
+        :class-card: feature-toggle-card
+
+        Temporal context networks that learn from unlabeled video.
+
+    .. grid-item-card:: ☁️ Cloud Ready
+        :class-card: feature-toggle-card
+
+        Browser-based labeling and training on headless GPU servers.
+
+.. rst-class:: multi-view-section
+
+Multi-view Capabilities
+------------------------
+
+* **Multi-View Transformer (MVT):** A unified architecture that enables simultaneous processing of information across all camera views through early-feature fusion.
+* **Patch Masking:** A novel training scheme that masks random image patches to force the model to learn robust cross-view correspondences.
+* **Geometric Consistency:** For calibrated setups, the framework incorporates 3D triangulation losses and geometrically-aware 3D data augmentation.
+* **Variance Inflation:** An advanced technique for outlier detection that identifies geometrically inconsistent predictions.
+
+.. rst-class:: single-view-section
+
+Single-view Capabilities
+-------------------------
+
+* **Temporal Context Networks:** Utilizes information from surrounding frames to resolve anatomical ambiguities and maintain tracking through brief occlusions.
+* **Unsupervised Learning:** Employs training objectives that penalize predictions for violating physical laws.
+* **Pretrained Backbone Support:** Optimized to work with generic, off-the-shelf Vision Transformer (ViT) backbones.
+
+.. rst-class:: cloud-section
+
+Cloud Application & Workflow
+-----------------------------
+
+* **Cloud & Headless Compatibility:** A browser-based interface designed for local or cloud deployment.
+* **Multi-view Labeling:** A specialized annotation tool that streamlines the labeling process by using camera calibration.
+* **Unified Multi-view Viewer:** Integrated visualization tools to inspect and compare predictions across all camera views simultaneously.
+
+.. raw:: html
+
+   <script>
+   document.addEventListener("DOMContentLoaded", function() {
+       const cards = document.querySelectorAll('.feature-toggle-card');
+       const detailSections = [
+           document.querySelector('.multi-view-section'),
+           document.querySelector('.single-view-section'),
+           document.querySelector('.cloud-section')
+       ];
+
+       function showSection(index) {
+           // Hide all sections and remove active styling from cards
+           detailSections.forEach((sec, i) => {
+               if (sec) sec.style.display = 'none';
+               cards[i].style.border = '1px solid var(--sd-color-card-border)';
+               cards[i].style.backgroundColor = 'transparent';
+           });
+
+           // Show the selected section
+           if (detailSections[index]) {
+               detailSections[index].style.display = 'block';
+               // Add active styling to card
+               cards[index].style.border = '2px solid #3498db';
+               cards[index].style.backgroundColor = 'rgba(52, 152, 219, 0.05)';
+           }
+       }
+
+       // Event listeners for clicks
+       cards.forEach((card, index) => {
+           card.style.cursor = 'pointer';
+           card.addEventListener('click', () => showSection(index));
+           card.addEventListener('mouseenter', () => showSection(index));
+           card.addEventListener('touchstart', () => showSection(index));
+
+       });
+
+       // Select the first card by default
+       showSection(0);
+   });
+   </script>
+
+   <style>
+   /* Enhance hover effect */
+   .feature-toggle-card:hover {
+       transform: translateY(-2px);
+       transition: all 0.2s ease;
+       box-shadow: 0 4px 12px rgba(0,0,0,0.1);
+   }
+   </style>
+
+
+--------
+
+Read the papers
+----------------
 
-If you would like to try out Lightning Pose, we provide a
-`Google Colab notebook <https://colab.research.google.com/github/paninski-lab/lightning-pose/blob/main/scripts/litpose_training_demo.ipynb>`_
-that steps through the process of training and evaluating a model on an example dataset
-- no data labeling or software installation required!
+The original Nature Methods 2024 paper that introduced Lightning Pose for single-view pose estimation using semisupervised learning and ensemble kalman smoothing (EKS):
 
-We also provide a
-`browser-based GUI <https://github.com/Lightning-Universe/Pose-app>`_
-that supports the full life cycle of a pose estimation project, from data annotation to model
-training to diagnostic visualizations.
+| **Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling and cloud-native open-source tools**
+| Biderman, D., Whiteway, M. R., Hurwitz, C., et al.
+
+.. grid::
+   :padding: 0
+   :margin: 2 0 0 0
+
+   .. grid-item::
+      .. button-link:: https://pmc.ncbi.nlm.nih.gov/articles/PMC12087009/
+         :color: primary
+         :outline:
+
+         *Nature Methods* 21, 1316–1328 (2024)
+
+The 2025 paper that added robust multiview support using multiview transformers (MVT),
+patch masking, 3d image augmentation and losses, and multiview EKS.
+
+| **An Uncertainty-Aware Framework for Data-Efficient Multi-View Animal Pose Estimation**
+| Aharon, L., Lee, K., et al.
+
+.. grid::
+   :padding: 0
+   :margin: 2 0 0 0
+
+   .. grid-item::
+      .. button-link:: https://arxiv.org/abs/2510.09903
+         :color: primary
+         :outline:
+
+         arXiv Preprint (2025)
+
+.. rst-class:: section-multi-view
+
+--------
+
+
+Get started with the app
+-------------------------
+
+The lightning pose app provides an easy-to-use GUI to access most lightning pose features.
+
+To get started, :doc:`install lightning pose <source/installation_guide>`
+and follow the :doc:`Create your first project <source/create_first_project>` tutorial.
+It covers the end-to-end workflow of labeling, training, and evaluation.
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
+   :hidden:
+
+   self
 
-   source/installation
-   source/user_guide/index
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: Getting started
+
+   source/installation_guide
+   source/core_concepts
+   source/create_first_project
+   source/example_data
+   source/importing_labeled_data
+
+.. toctree::
+   :maxdepth: 4
+   :hidden:
+   :caption: CLI User guide
+
+   source/user_guide_singleview/index
    source/user_guide_multiview/index
    source/user_guide_advanced/index
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: Community
+
    source/developer_guide/index
    source/faqs
-   source/api
-   source/cli
+   Release notes <https://github.com/paninski-lab/lightning-pose/releases>
+   source/migrating_to_app
 
-Indices and tables
-------------------
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: Reference
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   source/user_guide_singleview/config_file
+   source/api
+   source/cli_reference/index

docs/source/cli.rst

@@ -0,0 +1,9 @@
+.. _cli-crop:
+
+Crop
+----
+
+.. argparse::
+   :module: lightning_pose.cli.commands.crop
+   :func: get_parser
+   :prog: litpose crop

docs/source/cli_reference/crop.rst

@@ -0,0 +1,11 @@
+Lightning Pose command-line interface (CLI)
+==========================================
+
+.. toctree::
+   :maxdepth: 1
+
+   train
+   predict
+   crop
+   remap
+   run_app

docs/source/cli_reference/index.rst

@@ -0,0 +1,9 @@
+.. _cli-predict:
+
+Predict
+-------
+
+.. argparse::
+   :module: lightning_pose.cli.commands.predict
+   :func: get_parser
+   :prog: litpose predict

docs/source/cli_reference/predict.rst

@@ -0,0 +1,9 @@
+.. _cli-remap:
+
+Remap
+-----
+
+.. argparse::
+   :module: lightning_pose.cli.commands.remap
+   :func: get_parser
+   :prog: litpose remap

docs/source/cli_reference/remap.rst

@@ -0,0 +1,7 @@
+Run App
+-----
+
+.. argparse::
+   :module: lightning_pose.cli.commands.run_app
+   :func: get_parser
+   :prog: litpose run_app

docs/source/cli_reference/run_app.rst

@@ -0,0 +1,9 @@
+.. _cli-train:
+
+Train
+-----
+
+.. argparse::
+   :module: lightning_pose.cli.commands.train
+   :func: get_parser
+   :prog: litpose train