Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Enhancing the Resistance Welding of GF/PEI Composites via a PECVD-Deposited HMDSO Coating on a Heating Element.

ACS omega·2026
Same author

Helium Cold Atmospheric Plasma Causes Morphological and Biochemical Alterations in <i>Candida albicans</i> Cells.

Molecules (Basel, Switzerland)·2023
Same author

Study of a Conical Plasma Jet with a Cloth-Covered Nozzle for Polymer Treatment.

Polymers·2023
Same author

Simultaneous Treatment of Both Sides of the Polymer with a Conical-Shaped Atmospheric Pressure Plasma Jet.

Polymers·2023
Same author

Instrumented open-source filament extruder for research and education.

HardwareX·2022
Same author

Correlative light-electron fractography for fatigue striations characterization in metallic alloys.

Microscopy research and technique·2013

Related Experiment Video

Updated: May 20, 2026

Improved Methods for Preparing Transverse Sections and Unrolled Whole Mounts of Maize Leaf Primordia for Fluorescence and Confocal Imaging
06:11

Improved Methods for Preparing Transverse Sections and Unrolled Whole Mounts of Maize Leaf Primordia for Fluorescence and Confocal Imaging

Published on: September 22, 2023

Extended depth from focus reconstruction using NIH ImageJ plugins: quality and resolution of elevation maps.

Luis Rogerio De Oliveira Hein1, José Alberto De Oliveira, Kamila Amato De Campos

  • 1LAIMat-Materials Image Analysis Laboratory, DMT-Department of Materials and Technology, UNESP-Universidade Estadual Paulista, Guaratinguetá, São Paulo, Brazil. rhein@feg.unesp.br

Microscopy Research and Technique
|July 19, 2012
PubMed
Summary

This study optimized extended depth-from-focus (EDFR) plugins in ImageJ for creating elevation maps from microscopy images. Darkfield illumination and specific preprocessing enhance topographic measurement reliability.

More Related Videos

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography
08:04

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography

Published on: March 12, 2017

Three and Four-Dimensional Visualization and Analysis Approaches to Study Vertebrate Axial Elongation and Segmentation
12:59

Three and Four-Dimensional Visualization and Analysis Approaches to Study Vertebrate Axial Elongation and Segmentation

Published on: February 28, 2021

Related Experiment Videos

Last Updated: May 20, 2026

Improved Methods for Preparing Transverse Sections and Unrolled Whole Mounts of Maize Leaf Primordia for Fluorescence and Confocal Imaging
06:11

Improved Methods for Preparing Transverse Sections and Unrolled Whole Mounts of Maize Leaf Primordia for Fluorescence and Confocal Imaging

Published on: September 22, 2023

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography
08:04

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography

Published on: March 12, 2017

Three and Four-Dimensional Visualization and Analysis Approaches to Study Vertebrate Axial Elongation and Segmentation
12:59

Three and Four-Dimensional Visualization and Analysis Approaches to Study Vertebrate Axial Elongation and Segmentation

Published on: February 28, 2021

Area of Science:

  • Materials Science
  • Microscopy Imaging
  • Computational Imaging

Background:

  • Extended Depth-from-Focus (EDFR) techniques are crucial for reconstructing 3D information from microscopy image stacks.
  • Optimizing EDFR plugins and preprocessing methods is essential for accurate topographic analysis.

Purpose of the Study:

  • To compare and optimize NIH ImageJ plugins for EDFR based on spatial domain operations.
  • To evaluate preprocessing techniques for light microscopy image stacks to generate reliable elevation maps.

Main Methods:

  • Comparison of EDFR plugins using spatial domain operations on bright-field and darkfield image stacks.
  • Evaluation of preprocessing filters, including subtract background.
  • Analysis of image quality using signal-to-noise ratio, resolution, roughness, and fractal measurements.

Main Results:

  • Darkfield illumination improved image homogeneity and reduced variability in topographic measurements.
  • The subtract background filter enhanced image sharpness.
  • Larger kernel sizes in EDFR generally resulted in smoother height maps.

Conclusions:

  • Guidelines are established for generating reliable elevation maps from grayscale image stacks using light microscopy.
  • Darkfield illumination and appropriate preprocessing are recommended for robust topographic measurements.