Added high-level diagrams

.codeboarding/Core_Infrastructure.md

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+```mermaid
+
+graph LR
+
+    Versioning_Component["Versioning Component"]
+
+    Data_Types_and_Structures_Component["Data Types and Structures Component"]
+
+    Configuration_Management_Component["Configuration Management Component"]
+
+    Logging_and_System_Info_Component["Logging and System Info Component"]
+
+    Execution_Orchestration_Component["Execution Orchestration Component"]
+
+    Image_Level_Adjustment_Component["Image Level Adjustment Component"]
+
+    Versioning_Component -- "provides version to" --> Logging_and_System_Info_Component
+
+    Data_Types_and_Structures_Component -- "defines" --> Configuration_Management_Component
+
+    Data_Types_and_Structures_Component -- "consumed by" --> Execution_Orchestration_Component
+
+    Configuration_Management_Component -- "configures" --> Execution_Orchestration_Component
+
+    Configuration_Management_Component -- "provides settings to" --> Logging_and_System_Info_Component
+
+    Logging_and_System_Info_Component -- "records operations of" --> Execution_Orchestration_Component
+
+    Logging_and_System_Info_Component -- "reports on" --> Data_Types_and_Structures_Component
+
+    Execution_Orchestration_Component -- "uses" --> Configuration_Management_Component
+
+    Execution_Orchestration_Component -- "logs activities via" --> Logging_and_System_Info_Component
+
+    Image_Level_Adjustment_Component -- "processes" --> Data_Types_and_Structures_Component
+
+    Image_Level_Adjustment_Component -- "configured by" --> Configuration_Management_Component
+
+```
+
+
+
+[![CodeBoarding](https://img.shields.io/badge/Generated%20by-CodeBoarding-9cf?style=flat-square)](https://github.com/CodeBoarding/GeneratedOnBoardings)[![Demo](https://img.shields.io/badge/Try%20our-Demo-blue?style=flat-square)](https://www.codeboarding.org/demo)[![Contact](https://img.shields.io/badge/Contact%20us%20-%20contact@codeboarding.org-lightgrey?style=flat-square)](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+This section provides an overview of the `Core Infrastructure` components within the `starfish` project. These components are fundamental because they address the essential, cross-cutting concerns of the library, providing foundational services, defining core data representations, and offering basic utilities that higher-level modules depend on. They are not specific image processing algorithms but rather the underlying framework that enables the entire system to function robustly and consistently.
+
+
+
+### Versioning Component
+
+This component is responsible for programmatically determining and managing the version of the `starfish` software. It interacts with version control systems (like Git) to extract version information and format it according to standard conventions (e.g., PEP 440). This ensures that the software version can be consistently identified and reported.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/spacetx/starfish/starfish/core/_version.py#L0-L0" target="_blank" rel="noopener noreferrer">`starfish.core._version` (0:0)</a>
+
+
+
+
+
+### Data Types and Structures Component
+
+This component defines the fundamental data models, structures (e.g., `DecodedSpots`, `SpotAttributes`, `ValidatedTable`), and enumerations (e.g., `Axes`, `Levels`, `Coordinates`) used throughout the `starfish` library. It ensures consistent data representation and interoperability across different modules and algorithms.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/spacetx/starfish/starfish/core/starfish.py#L0-L0" target="_blank" rel="noopener noreferrer">`starfish.core.types` (0:0)</a>
+
+
+
+
+
+### Configuration Management Component
+
+This component handles the loading, parsing, and centralized management of application-wide configurations. It provides a flexible and centralized way to define and access parameters that control the behavior of various `starfish` algorithms and processes, supporting nested configuration structures.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/spacetx/starfish/starfish/core/starfish.py#L0-L0" target="_blank" rel="noopener noreferrer">`starfish.core.config` (0:0)</a>
+
+- <a href="https://github.com/spacetx/starfish/starfish/core/util/config.py#L0-L0" target="_blank" rel="noopener noreferrer">`starfish.core.util.config` (0:0)</a>
+
+
+
+
+
+### Logging and System Info Component
+
+This component provides comprehensive logging capabilities for the `starfish` application, enabling detailed tracking of execution flow, warnings, and errors. It also gathers system and dependency information, which is vital for diagnostics, error reporting, and understanding the execution environment.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/spacetx/starfish/starfish/core/util/logging.py#L0-L0" target="_blank" rel="noopener noreferrer">`starfish.core.util.logging` (0:0)</a>
+
+
+
+
+
+### Execution Orchestration Component
+
+This component is responsible for orchestrating the execution flow of different processing stages within the `starfish` pipeline. It manages the sequence of operations, ensuring proper order and dependencies, and can integrate utilities like timing for performance monitoring and optimization.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/spacetx/starfish/starfish/core/util/exec.py#L0-L0" target="_blank" rel="noopener noreferrer">`starfish.core.util.exec` (0:0)</a>
+
+
+
+
+
+### Image Level Adjustment Component
+
+This component offers a set of utility functions specifically designed for adjusting the intensity levels of images. This is a common and fundamental preprocessing step in image analysis pipelines, used to enhance contrast, normalize data, or prepare images for subsequent processing.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/spacetx/starfish/starfish/core/util/levels.py#L45-L119" target="_blank" rel="noopener noreferrer">`starfish.core.util.levels` (45:119)</a>
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)

.codeboarding/Experiment_Data_Core.md

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+```mermaid
+
+graph LR
+
+    Experiment["Experiment"]
+
+    FieldOfView["FieldOfView"]
+
+    ImageStack["ImageStack"]
+
+    Codebook["Codebook"]
+
+    StarfishConfig["StarfishConfig"]
+
+    SpaceTx_Validator["SpaceTx Validator"]
+
+    CropParameters["CropParameters"]
+
+    TileCollectionData["TileCollectionData"]
+
+    TileData["TileData"]
+
+    Experiment -- "contains" --> FieldOfView
+
+    Experiment -- "references" --> Codebook
+
+    Experiment -- "uses" --> StarfishConfig
+
+    Experiment -- "uses" --> SpaceTx_Validator
+
+    FieldOfView -- "manages" --> ImageStack
+
+    FieldOfView -- "uses" --> CropParameters
+
+    ImageStack -- "uses" --> CropParameters
+
+    ImageStack -- "composed of" --> TileCollectionData
+
+    TileCollectionData -- "composed of" --> TileData
+
+```
+
+
+
+[![CodeBoarding](https://img.shields.io/badge/Generated%20by-CodeBoarding-9cf?style=flat-square)](https://github.com/CodeBoarding/GeneratedOnBoardings)[![Demo](https://img.shields.io/badge/Try%20our-Demo-blue?style=flat-square)](https://www.codeboarding.org/demo)[![Contact](https://img.shields.io/badge/Contact%20us%20-%20contact@codeboarding.org-lightgrey?style=flat-square)](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+The `Experiment Data Core` subsystem in Starfish is designed to encapsulate and manage all data associated with a spatial transcriptomics experiment. It provides a structured, hierarchical representation of experimental data, from the top-level experiment down to individual image tiles, along with essential metadata and validation mechanisms. The chosen components are fundamental because they directly represent the data, define its structure, enable its interpretation, and ensure its integrity.
+
+
+
+### Experiment
+
+The top-level container representing an entire spatial transcriptomics experiment. It orchestrates access to all associated data, including multiple fields of view (FOVs) and the experiment's codebook. It provides methods for loading experiment data from standardized formats (e.g., JSON) and offers iterable access to its constituent FOVs.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/spacetx/starfish/starfish/core/experiment/experiment.py#L212-L453" target="_blank" rel="noopener noreferrer">`Experiment` (212:453)</a>
+
+
+
+
+
+### FieldOfView
+
+Represents a single field of view within an experiment, corresponding to a specific spatial region imaged. It acts as a direct interface to the raw imaging data for that region, providing methods to retrieve individual images or entire image stacks.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `FieldOfView` (1:1)
+
+
+
+
+
+### ImageStack
+
+A multi-dimensional array-like structure that holds the actual image data (raw or processed fluorescent images). It provides functionalities for accessing, manipulating, and iterating over image data across various dimensions (e.g., channels, imaging rounds, Z-planes). It's a core component for any image-based processing.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `ImageStack` (1:1)
+
+
+
+
+
+### Codebook
+
+Stores the mapping between fluorescent probes (or imaging channels) and the specific gene targets they represent. This information is critical for decoding the spatial transcriptomics data, translating raw intensity measurements into gene expression profiles. It can be loaded from a JSON format.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/spacetx/starfish/starfish/core/codebook/codebook.py#L28-L804" target="_blank" rel="noopener noreferrer">`Codebook` (28:804)</a>
+
+
+
+
+
+### StarfishConfig
+
+A centralized configuration management component for the Starfish application. It provides a structured way to store and retrieve various settings that influence the behavior of different parts of the software, including data loading, processing, and analysis.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `StarfishConfig` (1:1)
+
+
+
+
+
+### SpaceTx Validator
+
+A utility component responsible for validating the structure and content of experiment data against the SpaceTx format specification. This ensures that the input data adheres to predefined standards, promoting interoperability and data quality.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `SpaceTx Validator` (1:1)
+
+
+
+
+
+### CropParameters
+
+A data structure that defines the parameters for cropping image data. It specifies the region of interest to be extracted from a larger image stack, enabling focused analysis on specific parts of the field of view.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `CropParameters` (1:1)
+
+
+
+
+
+### TileCollectionData
+
+An internal class that manages the underlying data storage and access for collections of individual image tiles. It serves as a foundational layer for `ImageStack`, handling the organization and retrieval of image data chunks.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `TileCollectionData` (1:1)
+
+
+
+
+
+### TileData
+
+An internal class that manages the underlying data storage and access for individual image tiles. It represents a single chunk of image data and is a building block for `TileCollectionData`.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `TileData` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)