Version: 1.1
Binary download: Installer (for Windows 11)
Documentation: Read the Docs
Developer: Dr Marco Acevedo Z. (maaz.geologia@gmail.com)
Affiliation: School of Earth and Atmospheric Sciences, Queensland University of Technology
Date: 20-February-2026
Citation: Acevedo Zamora & Kamber 2023
Previous repository: Scripts repository
A geoscientific tool to interpret mineral phase maps elaborated with modern microcopy instrument software and image analysis pipelines. The user can investigate a mineral map and perform basic image analysis that is essential to study geological processes and is not available elsewhere for whole-slide images. The graphical user interfaces are designed to simplify the workflow.
Main:
Region of interest (ROI) annotator:
- Graphical User Interface (GUI) following three steps for reprocessing the input maps from QuPath
- Seamless selection of trained classifier outputs for each run
- Removal of the background class using the original names that are excluded from the analysis (e.g. hole, epoxy, cracks, mixed phases)
- Basic image processing to allow creating sample the foreground mask (e.g. dilation, rotation, mirroring) and checking the Preview
- Menu for editing mineral names of the ranked phases following a desired nomenclature (and resorting the targets)
- Focus the analysis on a region of interest (ROI) to avoid analysing uninteresting areas and reducing computational cost
- Varied pool of textural analysis: phase map, modal mineralogy, association, granulometry
- Automatic metadata extraction from input QuPath project containing:
- Saved pixel classifier - Process metadata and machine learning model saved in the QuPath > Classify > Pixel classification > Train pixel classifier
- Saved predicted map - File with the same basename as the classifier and often saved after classifying the entire sample (*.ome.tif) .
- Steps metadata - CSV files are saved tracking the semantic and numerical outputs from each processing step within the GUI and allow reproducibility.
- Grid design - adapts to the window size
- MatLab R2024b
- MatLab App Designer
- Additional libraries for metadata extraction:
*The standanlone App can be produced from:
Operating System: Microsoft Windows 11 Enterprise Version 10.0 (Build 22631) Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
- MATLAB Version 24.2 (R2024b)
- Computer Vision Toolbox Version 24.2 (R2024b)
- Curve Fitting Toolbox Version 24.2 (R2024b)
- Deep Learning Toolbox Version 24.2 (R2024b)
- Fixed-Point Designer Version 24.2 (R2024b)
- Global Optimization Toolbox Version 24.2 (R2024b)
- Image Processing Toolbox Version 24.2 (R2024b)
- MATLAB Compiler Version 24.2 (R2024b)
- Mapping Toolbox Version 24.2 (R2024b)
- Optimization Toolbox Version 24.2 (R2024b)
- Parallel Computing Toolbox Version 24.2 (R2024b)
- Signal Processing Toolbox Version 24.2 (R2024b)
- Statistics and Machine Learning Toolbox Version 24.2 (R2024b)
- Symbolic Math Toolbox Version 24.2 (R2024b)
- Wavelet Toolbox Version 24.2 (R2024b)
- Graphical user interface (GUI)
- Development script that allows trialling new implementation ideas before editing the GUI
- Open MatLab > App Designer
- Open "Phaseinterpreterv1.prj".
- Go to App Designer > Share > Standalone Desktop App.
- Within Apps required for your application to run, add the folders of the additional libraries (living within your PC).
- Click "Package" button while having selected "Runtime included in package" (for future users not having MatLab runtime).
- A folder "Phaseinterpreterv1" will appear containing:
- for_redistribution: installer that can be shared with others (users not having MatLab runtime)
- for_redistribution_files_only: executable (when having the runtime)
- for_testing: executable (when having the runtime)
- Contact me if:
- Requiring an example dataset to operate the software
- Having issues to compile or wanting to make a new branch/pull request that I need to revise
- This is a beta version that will soon be improved with user feedback
- If you are not familiar to coding but have a bunch of ideas, contact me
- I had in mind:
- Making TESCAN TIMA mineral liberation maps compatible with Phase interpreter
- Rewriting "Phase interpreter" in Python and enabling whole-slide imaging to match the capabilities of Cube converter, Chemistry simplifier, and QuPath
- I have not tried this software in Mac or Linux yet but it might be an easy fix
Thank you.
Marco