skip to main content


The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 5:00 PM ET until 11:00 PM ET on Friday, June 21 due to maintenance. We apologize for the inconvenience.

This content will become publicly available on March 1, 2025

Title: Image Analysis Methods for Grain Size Analysis : An Overview and A Case Study
The tools and techniques such as imaging and machine learning used in the measurement of many material and microstructural properties are rapidly evolving. In metals, the grain size is routinely measured to estimate the yield strength. This paper describes some of the algorithms used in processing the microstructures to conduct quantitative measurements. The image processing methods provide the possibility to go beyond calculating the ASTM grain size number and calculate the actual surface area of each grain, grain boundary length, and the shape of the grains. The image analysis methods can be very helpful in conducting detailed quantitative analysis with greater accuracy than many labour-intensive manual methods currently in use. The work describes the complexities in applying the imaging methods and approaches in the metallurgical and materials fields. Successful application of such methods can reduce the time and effort required to characterise microstructures and can provide more precise information.  more » « less
Award ID(s):
Author(s) / Creator(s):
; ; ; ; ; ;
Publisher / Repository:
The Institute of Indian Founrymen
Date Published:
Journal Name:
Indian foundry journal
Page Range / eLocation ID:
Subject(s) / Keyword(s):
["Image analysis","microstructure"]
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Background

    We performed a systematic review that identified at least 9,000 scientific papers on PubMed that include immunofluorescent images of cells from the central nervous system (CNS). These CNS papers contain tens of thousands of immunofluorescent neural images supporting the findings of over 50,000 associated researchers. While many existing reviews discuss different aspects of immunofluorescent microscopy, such as image acquisition and staining protocols, few papers discuss immunofluorescent imaging from an image-processing perspective. We analyzed the literature to determine the image processing methods that were commonly published alongside the associated CNS cell, microscopy technique, and animal model, and highlight gaps in image processing documentation and reporting in the CNS research field.


    We completed a comprehensive search of PubMed publications using Medical Subject Headings (MeSH) terms and other general search terms for CNS cells and common fluorescent microscopy techniques. Publications were found on PubMed using a combination of column description terms and row description terms. We manually tagged the comma-separated values file (CSV) metadata of each publication with the following categories: animal or cell model, quantified features, threshold techniques, segmentation techniques, and image processing software.


    Of the almost 9,000 immunofluorescent imaging papers identified in our search, only 856 explicitly include image processing information. Moreover, hundreds of the 856 papers are missing thresholding, segmentation, and morphological feature details necessary for explainable, unbiased, and reproducible results. In our assessment of the literature, we visualized current image processing practices, compiled the image processing options from the top twelve software programs, and designed a road map to enhance image processing. We determined that thresholding and segmentation methods were often left out of publications and underreported or underutilized for quantifying CNS cell research.


    Less than 10% of papers with immunofluorescent images include image processing in their methods. A few authors are implementing advanced methods in image analysis to quantify over 40 different CNS cell features, which can provide quantitative insights in CNS cell features that will advance CNS research. However, our review puts forward that image analysis methods will remain limited in rigor and reproducibility without more rigorous and detailed reporting of image processing methods.


    Image processing is a critical part of CNS research that must be improved to increase scientific insight, explainability, reproducibility, and rigor.

    more » « less
  2. Abstract

    Ever since the first image of a coral reef was captured in 1885, people worldwide have been accumulating images of coral reefscapes that document the historic conditions of reefs. However, these innumerable reefscape images suffer from perspective distortion, which reduces the apparent size of distant taxa, rendering the images unusable for quantitative analysis of reef conditions. Here we solve this century-long distortion problem by developing a novel computer-vision algorithm,ReScape, which removes the perspective distortion from reefscape images by transforming them into top-down views, making them usable for quantitative analysis of reef conditions. In doing so, we demonstrate the first-ever ecological application and extension of inverse-perspective mapping—a foundational technique used in the autonomous-driving industry. TheReScapealgorithm is composed of seven functions that (1) calibrate the camera lens, (2) remove the inherent lens-induced image distortions, (3) detect the scene’s horizon line, (4) remove the camera-roll angle, (5) detect the transformable reef area, (6) detect the scene’s perspective geometry, and (7) apply brute-force inverse-perspective mapping. The performance of theReScapealgorithm was evaluated by transforming the perspective of 125 reefscape images. Eighty-five percent of the images had no processing errors and of those, 95% were successfully transformed into top-down views.ReScapewas validated by demonstrating that same-length transects, placed increasingly further from the camera, became the same length after transformation. The mission of theReScapealgorithm is to (i) unlock historical information about coral-reef conditions from previously unquantified periods and localities, (ii) enable citizen scientists and recreational photographers to contribute reefscape images to the scientific process, and (iii) provide a new survey technique that can rigorously assess relatively large areas of coral reefs, and other marine and even terrestrial ecosystems, worldwide. To facilitate this mission, we compiled theReScapealgorithm into a free, user-friendly App that does not require any coding experience. Equipped with theReScapeApp, scientists can improve the management and prediction of the future of coral reefs by uncovering historical information from reefscape-image archives and by using reefscape images as a new, rapid survey method, opening a new era of coral-reef monitoring.

    more » « less
  3. Abstract Introduction

    Traction force microscopy (TFM) is a widely used technique to measure cell contractility on compliant substrates that mimic the stiffness of human tissues. For every step in a TFM workflow, users make choices which impact the quantitative results, yet many times the rationales and consequences for making these decisions are unclear. We have found few papers which show the complete experimental and mathematical steps of TFM, thus obfuscating the full effects of these decisions on the final output.


    Therefore, we present this “Field Guide” with the goal to explain the mathematical basis of common TFM methods to practitioners in an accessible way. We specifically focus on how errors propagate in TFM workflows given specific experimental design and analytical choices.


    We cover important assumptions and considerations in TFM substrate manufacturing, substrate mechanical properties, imaging techniques, image processing methods, approaches and parameters used in calculating traction stress, and data-reporting strategies.


    By presenting a conceptual review and analysis of TFM-focused research articles published over the last two decades, we provide researchers in the field with a better understanding of their options to make more informed choices when creating TFM workflows depending on the type of cell being studied. With this review, we aim to empower experimentalists to quantify cell contractility with confidence.

    more » « less
  4. Abstract

    Sparsity-based models and techniques have been exploited in many signal processing and imaging applications. Data-driven methods based on dictionary and sparsifying transform learning enable learning rich image features from data and can outperform analytical models. In particular, alternating optimization algorithms have been popular for learning such models. In this work, we focus on alternating minimization for a specific structured unitary sparsifying operator learning problem and provide a convergence analysis. While the algorithm converges to the critical points of the problem generally, our analysis establishes under mild assumptions, the local linear convergence of the algorithm to the underlying sparsifying model of the data. Analysis and numerical simulations show that our assumptions hold for standard probabilistic data models. In practice, the algorithm is robust to initialization.

    more » « less
  5. Summary

    Cancer is a heterogeneous disease. Finite mixture of regression (FMR)—as an important heterogeneity analysis technique when an outcome variable is present—has been extensively employed in cancer research, revealing important differences in the associations between a cancer outcome/phenotype and covariates. Cancer FMR analysis has been based on clinical, demographic, and omics variables. A relatively recent and alternative source of data comes from histopathological images. Histopathological images have been long used for cancer diagnosis and staging. Recently, it has been shown that high-dimensional histopathological image features, which are extracted using automated digital image processing pipelines, are effective for modeling cancer outcomes/phenotypes. Histopathological imaging–environment interaction analysis has been further developed to expand the scope of cancer modeling and histopathological imaging-based analysis. Motivated by the significance of cancer FMR analysis and a still strong demand for more effective methods, in this article, we take the natural next step and conduct cancer FMR analysis based on models that incorporate low-dimensional clinical/demographic/environmental variables, high-dimensional imaging features, as well as their interactions. Complementary to many of the existing studies, we develop a Bayesian approach for accommodating high dimensionality, screening out noises, identifying signals, and respecting the “main effects, interactions” variable selection hierarchy. An effective computational algorithm is developed, and simulation shows advantageous performance of the proposed approach. The analysis of The Cancer Genome Atlas data on lung squamous cell cancer leads to interesting findings different from the alternative approaches.

    more » « less