Updated README

Author: hschryver

README.md

@@ -1,17 +1,18 @@
 # Xenium Analysis Tools
 
-A Python library for processing and mapping Xenium sections using SpatialData formatting.
+A Python library for processing and analyzing Xenium sections, utilizing SpatialData formatting.
 
 ## Installation
 
-### Code Ocean Package Manager
+### In Code Ocean Package Manager:
 pip: git+[https://github.com/AllenInstitute/xenium_analysis_tools#egg=xenium-analysis-tools]
-
+* To get updated version of package, need to 'refresh' package image - usually removing and adding again works.
 
 ---
+## params.json
+Configurations for processing (folder/file names, MapMyCells parameters, options for functions, etc.)
 
 ## Modules
-
 ### 1. `process_xenium`
 
 Tools for processing raw Xenium outputs, managing SpatialData objects, and preparing data for downstream analysis.
@@ -20,18 +21,38 @@ Tools for processing raw Xenium outputs, managing SpatialData objects, and prepa
 * **`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.
+* **`process_spatialdata`**: Functions for processing/formatting Xenium `SpatialData` objects.
+* **`divide_sections`**: Functions for dividing multi-section slides into individual sections w/independent coordinate systems.
+* **`validate_sections`**: Quality control checks to ensure section processed correctly.
 
 ### 2. `map_xenium`
 
-Functions for mapping cell types to Xenium data using reference taxonomies.
+Tools for mapping cell types to Xenium data using reference taxonomies.
 
 #### 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.
+* **`map_dataset_sections`**: Map multiple sections in a dataset using MapMyCells.
+* **`map_sections`**: Functions for mapping cell types for an individual section.
 
 ### 3. `utils`
 Shared utility functions used across the library.
-* **`io_utils`**: Standardized functions for loading and saving Xenium data structures.
+* **`io_utils`**: Functions for loading data/organizing slides/sections, etc.
+
+## CO Capsules
+[generate_xenium_spatialdata](https://codeocean.allenneuraldynamics.org/capsule/8072328/tree)
+* Runs generate_dataset_slides
+
+[process_xenium_spatialdata](https://codeocean.allenneuraldynamics.org/capsule/4346497/tree)
+* Runs process_dataset_slides
+
+[map_xenium_types](https://codeocean.allenneuraldynamics.org/capsule/7531529/tree)
+* Runs map_dataset_sections
+
+[xenium_analysis_capsule](https://codeocean.allenneuraldynamics.org/capsule/7962049/tree) (currently updating...)
+* Capsule with notebooks for examples of how to work with SpatialData objects, explanations of processing steps, plotting, etc.
+
+## To-Dos:
+[ ]: Finish updating xenium_analysis_capsule
+
+[ ]: Consolidate & add Xenium data QC functions and make new capsule
+
+[ ]: Consolidate & add mapping evaluation/QC functions