Revise README for installation and usage clarity

Updated installation instructions and usage examples for clarity and accuracy.

Author: hschryver

README.md

@@ -1,111 +1,37 @@
-```markdown
 # Xenium Analysis Tools
 
-A Python library for processing and mapping Xenium spatial data, developed by the Allen Institute for Neural Dynamics.
+A Python library for processing and mapping Xenium sections using SpatialData formatting.
 
 ## Installation
 
-### Code Ocean Package Manager (Recommended)
-This library can be installed directly via the Code Ocean environment manager.
+### Code Ocean Package Manager
+pip: git+[https://github.com/AllenInstitute/xenium_analysis_tools#egg=xenium-analysis-tools]
 
-1. Open your Capsule.
-2. Go to the **Environment** tab.
-3. In the **Pip** section, click **Add**.
-4. Paste the following link:
-   ```text
-   git+[https://github.com/AllenInstitute/xenium_analysis_tools#egg=xenium-analysis-tools](https://github.com/AllenInstitute/xenium_analysis_tools#egg=xenium-analysis-tools)
-
-```
-
-5. Click **Launch Cloud Workstation** to build.
-
-### Local Installation
-
-To install locally or in a standard terminal:
-
-```bash
-pip install git+[https://github.com/AllenInstitute/xenium_analysis_tools.git](https://github.com/AllenInstitute/xenium_analysis_tools.git)
-
-```
 
 ---
 
 ## Modules
 
-The library is organized into three primary sub-packages designed to handle different stages of the Xenium analysis pipeline.
-
 ### 1. `process_xenium`
 
 Tools for processing raw Xenium outputs, managing SpatialData objects, and preparing data for downstream analysis.
 
-* **`process_dataset_slides`**: Main workflow for processing slides across an entire dataset.
+#### Main processing functions:
+* **`generate_dataset_slides`**: Generate the slide-level SpatialData objects from Xenium bundles for a Xenium dataset.
+* **`process_dataset_slides`**: Generate the section-level SpatialData objects from slides for a Xenium dataset.
+#### Task-specific functions:
 * **`process_spatialdata`**: Core logic for manipulating and formatting Xenium `SpatialData` objects.
 * **`divide_sections`**: Utilities for handling section boundaries and splitting data.
 * **`validate_sections`**: Quality control checks to ensure section integrity before processing.
-* **`generate_dataset_slides`**: Helper functions for creating slide-level representations.
 
 ### 2. `map_xenium`
 
 Functions for mapping cell types to Xenium data using reference taxonomies.
 
-* **`map_sections`**: Logic for mapping cell types on individual tissue sections.
+#### Main processing function:
 * **`map_dataset_sections`**: Batch processing tools to apply mapping across multiple sections in a dataset.
+* **`map_sections`**: Logic for mapping cell types on individual sections.
 
 ### 3. `utils`
-
 Shared utility functions used across the library.
-
 * **`io_utils`**: Standardized functions for loading and saving Xenium data structures.
-
----
-
-## Usage
-
-Import the specific modules you need for your analysis workflow.
-
-**Example: Processing a Dataset**
-
-```python
-from xenium_analysis_tools.process_xenium import process_dataset_slides
-from xenium_analysis_tools.utils import io_utils
-
-# Load your configuration or data path
-data_path = "/path/to/xenium/data"
-
-# Run the processing pipeline
-process_dataset_slides.run(data_path)
-
-```
-
-**Example: Mapping Sections**
-
-```python
-from xenium_analysis_tools.map_xenium import map_dataset_sections
-
-# Run cell type mapping on processed sections
-map_dataset_sections.run_mapping(
-    processed_data_path="/path/to/processed/data",
-    taxonomy_ref="/path/to/taxonomy"
-)
-
-```
-
----
-
-## Development
-
-### Updating the Package
-
-1. Make changes to the code in the `src/` directory.
-2. Bump the version in `src/xenium_analysis_tools/__init__.py`.
-3. Commit and push to GitHub.
-4. Create and push a new tag matching the version (e.g., `v0.1.1`).
-
-### Running Tests
-
-This project uses `pytest`. Run the following in the root directory:
-
-```bash
-pytest tests/
-
-```