chore: Add new readme section and dev_doc file (#1101)

Co-authored-by: rainandbare <[email protected]>

.infra/rdev/values.yaml

@@ -2,7 +2,7 @@ stack:
   services:
     explorer:
       image:
-        tag: sha-f55da22f
+        tag: sha-da511850
       replicaCount: 1
       env:
         # env vars common to all deployment stages

README.md

@@ -10,6 +10,15 @@ CZ CELLxGENE Explorer (pronounced "cell-by-gene") is an interactive data explore
 
 Whether you need to visualize one thousand cells or one million, CELLxGENE Explorer helps you gain insight into your single-cell data.
 
+#### Highlighted Features
+
+- **Interactive Exploration**: Provides intuitive navigation of 2D matrices with dimensions, allowing users to explore datasets.
+- **Data Visualization**: Offers clear, intuitive visual representations of datasets and related artifacts.
+- **Spatial Mode with Deep Zoom**: Enables seamless zooming in and out of high-resolution images & spatial data (e.g., Slide-seq V2, Visium) to examine fine details.
+- **Gating/Selection**: Allows users to sub-select data and integrate multiple selections.
+- **Dynamic**: Users can create their own gene sets to investigate.
+- **Analytics**: Provides on-demand, interactive analytical tools such as differential expression analysis (gene/var t-tests).
+
 ## Getting started
 
 ### The comprehensive guide to CZ CELLxGENE
@@ -37,10 +46,17 @@ For any errors, [report bugs on Github](https://github.com/chanzuckerberg/single
 
 ### Contributing
 
-Please see our [contributing guide](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) and don't hesitate to open an issue or send a pull request to improve CZ CELLxGENE Explorer. Please see the [dev_docs](https://github.com/chanzuckerberg/single-cell-explorer/blob/main/dev_docs) for pull request suggestions, unit test details, local documentation preview, and other development specifics. 
+Please see our [contributing guide](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) and don't hesitate to open an issue or send a pull request to improve CZ CELLxGENE Explorer.
 
 This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/master/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [email protected].
 
+#### Start Here
+- [Set Up Local Dev Environment](https://github.com/chanzuckerberg/single-cell-explorer/blob/main/dev_docs/developer_guidelines.md)
+- [Design Principles](https://github.com/chanzuckerberg/single-cell-explorer/blob/main/dev_docs/design_principles.md)
+- [How to write Tests](https://github.com/chanzuckerberg/single-cell-explorer/blob/main/dev_docs/e2e_tests.md)
+- [Pull Request Suggestions](https://github.com/chanzuckerberg/single-cell-explorer/blob/main/dev_docs/pull_request_guidelines.md)
+- ...and [more](https://github.com/chanzuckerberg/single-cell-explorer/blob/main/dev_docs)
+
 ### Reuse
 
 This project was started with the sole goal of empowering the scientific community to explore and understand their data. 

dev_docs/deep_zoom.md

@@ -0,0 +1,32 @@
+# Spatial Mode Deep Zoom Feature
+
+The Deep Zoom feature in CELLxGENE Explorer enhances the spatial exploration of datasets by allowing users to zoom in and out of high-resolution images smoothly. This functionality is critical for detailed examination of spatial data, such as those from Visium, providing fine-grained insight into tissue samples and cellular interactions.
+
+It is built on the OpenSeadragon (OSD) JavaScript library, integrated into the Explorer’s frontend to deliver a responsive zooming experience. The backend handles the generation and storage of deep zoom image tiles, making it efficient to load and view high-resolution spatial data across environments (dev, staging, prod).
+
+## Frontend Integration (Explorer FE)
+
+- [OpenSeadragon (OSD)](https://openseadragon.github.io/): The OSD library is imported into the frontend to handle interactive zoom and pan operations. OSD dynamically loads image tiles based on the user’s zoom level and position.
+- Zoom & Pan Synchronization: Zooming and panning are kept in sync with spatial layers (e.g., dot layers) in the Explorer to ensure smooth interaction across different dataset views.
+- Dynamic Resource Loading: URLs for the image tiles are generated based on the current environment (dev, staging, prod), ensuring the correct assets are fetched dynamically.
+
+## Backend Image Processing & Storage
+
+- CXG Conversion Script: The backend uses a CXG conversion pipeline to process high-resolution spatial images and generate the necessary image tiles and manifest files (DZI format) for deep zoom.
+- Metadata API: Sends some metadata like image_width, image_height, resolution, scaleref etc. used in dot size calculation & normalizes spatial embedding so it aligns with the image underlay.
+- Storage on S3: The generated deep zoom assets (tiles and DZI files) are uploaded to a dedicated Amazon S3 bucket (spatial-deep-zoom). Each dataset has its own folder in the bucket (e.g., spatial-deep-zoom/{DATASET_VERSION_ID}). Note: The DATASET_VERSION_ID includes a dataset's revisions while a DATASET_ID does not.
+
+## Content Delivery
+
+- AWS CloudFront: CloudFront is used to cache and deliver deep zoom assets, improving performance by serving assets from the nearest available server to the user. This minimizes latency, ensuring a smooth experience during zooming and panning.
+
+## Validation & Testing
+
+- Frontend Tests: Screenshot testing ensures correct tile rendering across different zoom levels. E2E testing verifies that image export, toggle, and panning features work seamlessly.
+- Backend Tests: Ensure that the CXG conversion process correctly generates deep zoom tiles, uploads them to S3, and that CloudFront caches the assets properly.
+
+### Resources and Links
+
+[Spatial Mode Deep Zooming Tech Spec Design Doc](https://docs.google.com/document/d/1Jp5ePtAk6uXYZjY8XVkdfr0jf1IG0MJj8H_clPuRdFY)
+
+[CELLxGENE Platform Technical Overview](https://docs.google.com/document/d/19IZbojtc7eofV75NnL5C6fCgBJB13KIswWNOn12xAa0)