Livermore SEM Image Tools (LIST)

Scanning Electron Microscopy (SEM) images provide a variety of structural and morphological information for the characterization of the nanomaterials in material science and chemistry communities. This code offers automatic recognition and quantitative analysis of SEM images in a high-throughput manner using computer vision and machine learning techniques. The main function of this application is to extract particle size and morphology information of overlapping nanoparticles and core-shell nanostructures in a user friendly interface. The code is written in C++ with QT environment, and has been tested on MacOSX.

Getting Started

Prerequisites for source compilation

• QT 5 or higher
• OpenCV 4 or higher
• Tesseract (with JPEG library)
• Persistence1d.hpp

Running the application

The following files are required to run the application:

• EAST detector checkpoint: frozen_east_text_detection.pb, see argman/EAST on gitHub for more detail
• Tesseract trained data: eng.traineddata, osd.traineddata, snum.traineddata, see tesseract-ocr on GitHub for more detail

These files can be also found here

Deployment

How to make a DMG installer for MacOSX distribution

1. use this keyword in pro: CONFIG += app_bundle
2. run: macdeployqt LIST.app -dmg (make sure to use macdeploygt from the same QT directory)
3. copy any missing dylib to "LIST.app/Contents/Frameworks" manually. For example, the followings need to be copied manually.
   libopencv_core.4.1.1.dylib libopencv_core.4.1.dylib libopencv_core.dylib libopencv_dnn.4.1.1.dylib libopencv_dnn.4.1.dylib libopencv_dnn.dylib libopencv_imgcodecs.4.1.1.dylib libopencv_imgcodecs.4.1.dylib libopencv_imgcodecs.dylib libopencv_imgproc.4.1.1.dylib libopencv_imgproc.4.1.dylib libopencv_imgproc.dylib libtesseract.4.dylib
4. copy EAST descriptor and tesseract trained data ("frozen_east_text_detection.pb", "eng.traineddata", "osd.traineddata", "snum.traineddata") to "LIST.app/Contents/Resources"
5. copy "src/LIST.ini" to "LIST.app/Contents/MacOS"
6. copy sample SEM images to "LIST.app/Samples" (optional)
7. run again: macdeployqt LIST.app -dmg (make sure to use macdeploygt from the same QT directory)

A precompiled DMG file as a MacOSX bundle can be found here

Contributing

To contribute to LIST, please send us a pull request. When you send your request, make develop the destination branch on the repository.

Versioning

0.9

Authors

LIST was created by Hyojin Kim, hkim@llnl.gov.

Other contributors

Special thanks to Jinkyu Han (han10@llnl.gov) for extensive program tests and suggestions.

This project was supported by a LLNL's lab directed research and development - strategic initiatives project (Accelerating Feedstock Optimization Using Computer Vision, Machine Learning, and Data Analytic Techniques, PI: T. Yong Han).

Citing LIST

If you need to reference LIST in a publication, please cite the following paper:

Hyojin Kim, Jinkyu Han, T. Yong Han, "Machine Vision-Driven Automatic Recognition of Particle Size and Morphology in SEM Images", Nanoscale, 2020, 10.1039/D0NR04140H

License

LIST is distributed under the terms of the MIT license. All new contributions must be made under this license.

SPDX-License-Identifier: MIT

LLNL-CODE-806098