Data and code from: Wide-Angle Lung Experiment Segmentation (WALES): A novel methodology for quantitative assessment of lung pathology in model systems

For pre-clinical studies, the standard practice for evaluating lung injury usually involves an assessment of pulmonary histopathology by a certified pathologist. This is typically accomplished by light microscopy using a semi-quantitative 4-point scale. In contrast, automated image analysis software allows a more quantitative assessment, though inherent limitations with such automated programs can produce misleading conclusions. For example, specific imaging features may be incorrectly scored or classified within the specimen because of the complex architecture and heterogenous structures present in the lung. Additionally, tissue processing and handling may further introduce artifacts and inconsistencies that affect automated analysis. To address these limitations, we developed a novel lung image analysis program, Wide Angle Lung Experiment Segmentation (WALES), which employs Meta’s Segment Anything Model to provide semi-automated masking and relative density analysis to efficiently qua..., , , # WALES GUI and Analysis

## Overview

This repository contains the code required to complete analysis using WALES & all related data.

The repository is divided into two main parts:

1. **Analysis.zip:** Contains the datasets, processed images, and results from various experiments.
2. **WALES_GUI_code.zip:** Contains the Python scripts, notebooks, and required files to run the WALES analysis GUI.

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## Repository Structure

The repository is organized as follows:

* `Analysis/`
* Contains sub-folders for different experimental analyses (`Homogenous`, `Inflation`, `Main_Analysis`, `TRI_vs_H&E`). Each sub-folder generally includes `Original_Images`, `Masked`, `Thresholded`, and analysis results (`heatmaps`, `.csv`, `.txt` files).
* `WALES_GUI_code/`
* Contains the source code and necessary files for the WALES image analysis tools.

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### Analysis Folder Structure

Within the `Analysis/` directory, experiments are separated:

* `Analysis/Main_Analysis/`
* The primary analysis ...