Add directory tree structure description.

README.md

@@ -16,10 +16,6 @@ DIMA provides reusable operations for data integration, manipulation, and extrac
 4. **Jupyter notebooks**
   Demonstrates DIMA’s core functionalities, such as data integration, HDF5 file creation, visualization, and metadata annotation. Key notebooks include examples for data sharing, OpenBis ETL, and workflow demos. 
 
-## Repository Structure
-
-
-
 ## Requirements
 
 For **Windows** users, the following are required:
@@ -66,7 +62,29 @@ Open **Anaconda Prompt** or a terminal with access to conda.
    conda env create --file environment.yml
    ```
 
-## Software arquitecture
+## Repository Structure and Software arquitecture
+
+**Directories**
+
+  - `input_files/` stores some example raw input data or campaign descriptor YAML files.
+
+  - `output_files/` stores generated outputs for local processing. 
+
+  - `instruments/` contains instrument-specific dictionaries and file readers.
+
+  - `src/` contains the main source code, HDF5 Writer and Data Operations Manager.
+
+  - `utils/` contains generic data conversion operations, supporting the source code.
+
+  - `notebooks/` contains a collection of Jupyter notebooks, demonstrating DIMA's main functionalities.
+
+  - `pipelines/` contains source code for the data integration pipeline and metadata revision workflow.
+
+  - `visualization/` contains primarily functions for visualization of HDF5 files as treemaps. 
+
+---
+
+**Software arquitecture**
 
 <p align="center">
   <img src="docs/software_arquitecture_diagram.svg" alt="Alt Text">