- •Preface
- •Imaging Microscopic Features
- •Measuring the Crystal Structure
- •References
- •Contents
- •1.4 Simulating the Effects of Elastic Scattering: Monte Carlo Calculations
- •What Are the Main Features of the Beam Electron Interaction Volume?
- •How Does the Interaction Volume Change with Composition?
- •How Does the Interaction Volume Change with Incident Beam Energy?
- •How Does the Interaction Volume Change with Specimen Tilt?
- •1.5 A Range Equation To Estimate the Size of the Interaction Volume
- •References
- •2: Backscattered Electrons
- •2.1 Origin
- •2.2.1 BSE Response to Specimen Composition (η vs. Atomic Number, Z)
- •SEM Image Contrast with BSE: “Atomic Number Contrast”
- •SEM Image Contrast: “BSE Topographic Contrast—Number Effects”
- •2.2.3 Angular Distribution of Backscattering
- •Beam Incident at an Acute Angle to the Specimen Surface (Specimen Tilt > 0°)
- •SEM Image Contrast: “BSE Topographic Contrast—Trajectory Effects”
- •2.2.4 Spatial Distribution of Backscattering
- •Depth Distribution of Backscattering
- •Radial Distribution of Backscattered Electrons
- •2.3 Summary
- •References
- •3: Secondary Electrons
- •3.1 Origin
- •3.2 Energy Distribution
- •3.3 Escape Depth of Secondary Electrons
- •3.8 Spatial Characteristics of Secondary Electrons
- •References
- •4: X-Rays
- •4.1 Overview
- •4.2 Characteristic X-Rays
- •4.2.1 Origin
- •4.2.2 Fluorescence Yield
- •4.2.3 X-Ray Families
- •4.2.4 X-Ray Nomenclature
- •4.2.6 Characteristic X-Ray Intensity
- •Isolated Atoms
- •X-Ray Production in Thin Foils
- •X-Ray Intensity Emitted from Thick, Solid Specimens
- •4.3 X-Ray Continuum (bremsstrahlung)
- •4.3.1 X-Ray Continuum Intensity
- •4.3.3 Range of X-ray Production
- •4.4 X-Ray Absorption
- •4.5 X-Ray Fluorescence
- •References
- •5.1 Electron Beam Parameters
- •5.2 Electron Optical Parameters
- •5.2.1 Beam Energy
- •Landing Energy
- •5.2.2 Beam Diameter
- •5.2.3 Beam Current
- •5.2.4 Beam Current Density
- •5.2.5 Beam Convergence Angle, α
- •5.2.6 Beam Solid Angle
- •5.2.7 Electron Optical Brightness, β
- •Brightness Equation
- •5.2.8 Focus
- •Astigmatism
- •5.3 SEM Imaging Modes
- •5.3.1 High Depth-of-Field Mode
- •5.3.2 High-Current Mode
- •5.3.3 Resolution Mode
- •5.3.4 Low-Voltage Mode
- •5.4 Electron Detectors
- •5.4.1 Important Properties of BSE and SE for Detector Design and Operation
- •Abundance
- •Angular Distribution
- •Kinetic Energy Response
- •5.4.2 Detector Characteristics
- •Angular Measures for Electron Detectors
- •Elevation (Take-Off) Angle, ψ, and Azimuthal Angle, ζ
- •Solid Angle, Ω
- •Energy Response
- •Bandwidth
- •5.4.3 Common Types of Electron Detectors
- •Backscattered Electrons
- •Passive Detectors
- •Scintillation Detectors
- •Semiconductor BSE Detectors
- •5.4.4 Secondary Electron Detectors
- •Everhart–Thornley Detector
- •Through-the-Lens (TTL) Electron Detectors
- •TTL SE Detector
- •TTL BSE Detector
- •Measuring the DQE: BSE Semiconductor Detector
- •References
- •6: Image Formation
- •6.1 Image Construction by Scanning Action
- •6.2 Magnification
- •6.3 Making Dimensional Measurements With the SEM: How Big Is That Feature?
- •Using a Calibrated Structure in ImageJ-Fiji
- •6.4 Image Defects
- •6.4.1 Projection Distortion (Foreshortening)
- •6.4.2 Image Defocusing (Blurring)
- •6.5 Making Measurements on Surfaces With Arbitrary Topography: Stereomicroscopy
- •6.5.1 Qualitative Stereomicroscopy
- •Fixed beam, Specimen Position Altered
- •Fixed Specimen, Beam Incidence Angle Changed
- •6.5.2 Quantitative Stereomicroscopy
- •Measuring a Simple Vertical Displacement
- •References
- •7: SEM Image Interpretation
- •7.1 Information in SEM Images
- •7.2.2 Calculating Atomic Number Contrast
- •Establishing a Robust Light-Optical Analogy
- •Getting It Wrong: Breaking the Light-Optical Analogy of the Everhart–Thornley (Positive Bias) Detector
- •Deconstructing the SEM/E–T Image of Topography
- •SUM Mode (A + B)
- •DIFFERENCE Mode (A−B)
- •References
- •References
- •9: Image Defects
- •9.1 Charging
- •9.1.1 What Is Specimen Charging?
- •9.1.3 Techniques to Control Charging Artifacts (High Vacuum Instruments)
- •Observing Uncoated Specimens
- •Coating an Insulating Specimen for Charge Dissipation
- •Choosing the Coating for Imaging Morphology
- •9.2 Radiation Damage
- •9.3 Contamination
- •References
- •10: High Resolution Imaging
- •10.2 Instrumentation Considerations
- •10.4.1 SE Range Effects Produce Bright Edges (Isolated Edges)
- •10.4.4 Too Much of a Good Thing: The Bright Edge Effect Hinders Locating the True Position of an Edge for Critical Dimension Metrology
- •10.5.1 Beam Energy Strategies
- •Low Beam Energy Strategy
- •High Beam Energy Strategy
- •Making More SE1: Apply a Thin High-δ Metal Coating
- •Making Fewer BSEs, SE2, and SE3 by Eliminating Bulk Scattering From the Substrate
- •10.6 Factors That Hinder Achieving High Resolution
- •10.6.2 Pathological Specimen Behavior
- •Contamination
- •Instabilities
- •References
- •11: Low Beam Energy SEM
- •11.3 Selecting the Beam Energy to Control the Spatial Sampling of Imaging Signals
- •11.3.1 Low Beam Energy for High Lateral Resolution SEM
- •11.3.2 Low Beam Energy for High Depth Resolution SEM
- •11.3.3 Extremely Low Beam Energy Imaging
- •References
- •12.1.1 Stable Electron Source Operation
- •12.1.2 Maintaining Beam Integrity
- •12.1.4 Minimizing Contamination
- •12.3.1 Control of Specimen Charging
- •12.5 VPSEM Image Resolution
- •References
- •13: ImageJ and Fiji
- •13.1 The ImageJ Universe
- •13.2 Fiji
- •13.3 Plugins
- •13.4 Where to Learn More
- •References
- •14: SEM Imaging Checklist
- •14.1.1 Conducting or Semiconducting Specimens
- •14.1.2 Insulating Specimens
- •14.2 Electron Signals Available
- •14.2.1 Beam Electron Range
- •14.2.2 Backscattered Electrons
- •14.2.3 Secondary Electrons
- •14.3 Selecting the Electron Detector
- •14.3.2 Backscattered Electron Detectors
- •14.3.3 “Through-the-Lens” Detectors
- •14.4 Selecting the Beam Energy for SEM Imaging
- •14.4.4 High Resolution SEM Imaging
- •Strategy 1
- •Strategy 2
- •14.5 Selecting the Beam Current
- •14.5.1 High Resolution Imaging
- •14.5.2 Low Contrast Features Require High Beam Current and/or Long Frame Time to Establish Visibility
- •14.6 Image Presentation
- •14.6.1 “Live” Display Adjustments
- •14.6.2 Post-Collection Processing
- •14.7 Image Interpretation
- •14.7.1 Observer’s Point of View
- •14.7.3 Contrast Encoding
- •14.8.1 VPSEM Advantages
- •14.8.2 VPSEM Disadvantages
- •15: SEM Case Studies
- •15.1 Case Study: How High Is That Feature Relative to Another?
- •15.2 Revealing Shallow Surface Relief
- •16.1.2 Minor Artifacts: The Si-Escape Peak
- •16.1.3 Minor Artifacts: Coincidence Peaks
- •16.1.4 Minor Artifacts: Si Absorption Edge and Si Internal Fluorescence Peak
- •16.2 “Best Practices” for Electron-Excited EDS Operation
- •16.2.1 Operation of the EDS System
- •Choosing the EDS Time Constant (Resolution and Throughput)
- •Choosing the Solid Angle of the EDS
- •Selecting a Beam Current for an Acceptable Level of System Dead-Time
- •16.3.1 Detector Geometry
- •16.3.2 Process Time
- •16.3.3 Optimal Working Distance
- •16.3.4 Detector Orientation
- •16.3.5 Count Rate Linearity
- •16.3.6 Energy Calibration Linearity
- •16.3.7 Other Items
- •16.3.8 Setting Up a Quality Control Program
- •Using the QC Tools Within DTSA-II
- •Creating a QC Project
- •Linearity of Output Count Rate with Live-Time Dose
- •Resolution and Peak Position Stability with Count Rate
- •Solid Angle for Low X-ray Flux
- •Maximizing Throughput at Moderate Resolution
- •References
- •17: DTSA-II EDS Software
- •17.1 Getting Started With NIST DTSA-II
- •17.1.1 Motivation
- •17.1.2 Platform
- •17.1.3 Overview
- •17.1.4 Design
- •Simulation
- •Quantification
- •Experiment Design
- •Modeled Detectors (. Fig. 17.1)
- •Window Type (. Fig. 17.2)
- •The Optimal Working Distance (. Figs. 17.3 and 17.4)
- •Elevation Angle
- •Sample-to-Detector Distance
- •Detector Area
- •Crystal Thickness
- •Number of Channels, Energy Scale, and Zero Offset
- •Resolution at Mn Kα (Approximate)
- •Azimuthal Angle
- •Gold Layer, Aluminum Layer, Nickel Layer
- •Dead Layer
- •Zero Strobe Discriminator (. Figs. 17.7 and 17.8)
- •Material Editor Dialog (. Figs. 17.9, 17.10, 17.11, 17.12, 17.13, and 17.14)
- •17.2.1 Introduction
- •17.2.2 Monte Carlo Simulation
- •17.2.4 Optional Tables
- •References
- •18: Qualitative Elemental Analysis by Energy Dispersive X-Ray Spectrometry
- •18.1 Quality Assurance Issues for Qualitative Analysis: EDS Calibration
- •18.2 Principles of Qualitative EDS Analysis
- •Exciting Characteristic X-Rays
- •Fluorescence Yield
- •X-ray Absorption
- •Si Escape Peak
- •Coincidence Peaks
- •18.3 Performing Manual Qualitative Analysis
- •Beam Energy
- •Choosing the EDS Resolution (Detector Time Constant)
- •Obtaining Adequate Counts
- •18.4.1 Employ the Available Software Tools
- •18.4.3 Lower Photon Energy Region
- •18.4.5 Checking Your Work
- •18.5 A Worked Example of Manual Peak Identification
- •References
- •19.1 What Is a k-ratio?
- •19.3 Sets of k-ratios
- •19.5 The Analytical Total
- •19.6 Normalization
- •19.7.1 Oxygen by Assumed Stoichiometry
- •19.7.3 Element by Difference
- •19.8 Ways of Reporting Composition
- •19.8.1 Mass Fraction
- •19.8.2 Atomic Fraction
- •19.8.3 Stoichiometry
- •19.8.4 Oxide Fractions
- •Example Calculations
- •19.9 The Accuracy of Quantitative Electron-Excited X-ray Microanalysis
- •19.9.1 Standards-Based k-ratio Protocol
- •19.9.2 “Standardless Analysis”
- •19.10 Appendix
- •19.10.1 The Need for Matrix Corrections To Achieve Quantitative Analysis
- •19.10.2 The Physical Origin of Matrix Effects
- •19.10.3 ZAF Factors in Microanalysis
- •X-ray Generation With Depth, φ(ρz)
- •X-ray Absorption Effect, A
- •X-ray Fluorescence, F
- •References
- •20.2 Instrumentation Requirements
- •20.2.1 Choosing the EDS Parameters
- •EDS Spectrum Channel Energy Width and Spectrum Energy Span
- •EDS Time Constant (Resolution and Throughput)
- •EDS Calibration
- •EDS Solid Angle
- •20.2.2 Choosing the Beam Energy, E0
- •20.2.3 Measuring the Beam Current
- •20.2.4 Choosing the Beam Current
- •Optimizing Analysis Strategy
- •20.3.4 Ba-Ti Interference in BaTiSi3O9
- •20.4 The Need for an Iterative Qualitative and Quantitative Analysis Strategy
- •20.4.2 Analysis of a Stainless Steel
- •20.5 Is the Specimen Homogeneous?
- •20.6 Beam-Sensitive Specimens
- •20.6.1 Alkali Element Migration
- •20.6.2 Materials Subject to Mass Loss During Electron Bombardment—the Marshall-Hall Method
- •Thin Section Analysis
- •Bulk Biological and Organic Specimens
- •References
- •21: Trace Analysis by SEM/EDS
- •21.1 Limits of Detection for SEM/EDS Microanalysis
- •21.2.1 Estimating CDL from a Trace or Minor Constituent from Measuring a Known Standard
- •21.2.2 Estimating CDL After Determination of a Minor or Trace Constituent with Severe Peak Interference from a Major Constituent
- •21.3 Measurements of Trace Constituents by Electron-Excited Energy Dispersive X-ray Spectrometry
- •The Inevitable Physics of Remote Excitation Within the Specimen: Secondary Fluorescence Beyond the Electron Interaction Volume
- •Simulation of Long-Range Secondary X-ray Fluorescence
- •NIST DTSA II Simulation: Vertical Interface Between Two Regions of Different Composition in a Flat Bulk Target
- •NIST DTSA II Simulation: Cubic Particle Embedded in a Bulk Matrix
- •21.5 Summary
- •References
- •22.1.2 Low Beam Energy Analysis Range
- •22.2 Advantage of Low Beam Energy X-Ray Microanalysis
- •22.2.1 Improved Spatial Resolution
- •22.3 Challenges and Limitations of Low Beam Energy X-Ray Microanalysis
- •22.3.1 Reduced Access to Elements
- •22.3.3 At Low Beam Energy, Almost Everything Is Found To Be Layered
- •Analysis of Surface Contamination
- •References
- •23: Analysis of Specimens with Special Geometry: Irregular Bulk Objects and Particles
- •23.2.1 No Chemical Etching
- •23.3 Consequences of Attempting Analysis of Bulk Materials With Rough Surfaces
- •23.4.1 The Raw Analytical Total
- •23.4.2 The Shape of the EDS Spectrum
- •23.5 Best Practices for Analysis of Rough Bulk Samples
- •23.6 Particle Analysis
- •Particle Sample Preparation: Bulk Substrate
- •The Importance of Beam Placement
- •Overscanning
- •“Particle Mass Effect”
- •“Particle Absorption Effect”
- •The Analytical Total Reveals the Impact of Particle Effects
- •Does Overscanning Help?
- •23.6.6 Peak-to-Background (P/B) Method
- •Specimen Geometry Severely Affects the k-ratio, but Not the P/B
- •Using the P/B Correspondence
- •23.7 Summary
- •References
- •24: Compositional Mapping
- •24.2 X-Ray Spectrum Imaging
- •24.2.1 Utilizing XSI Datacubes
- •24.2.2 Derived Spectra
- •SUM Spectrum
- •MAXIMUM PIXEL Spectrum
- •24.3 Quantitative Compositional Mapping
- •24.4 Strategy for XSI Elemental Mapping Data Collection
- •24.4.1 Choosing the EDS Dead-Time
- •24.4.2 Choosing the Pixel Density
- •24.4.3 Choosing the Pixel Dwell Time
- •“Flash Mapping”
- •High Count Mapping
- •References
- •25.1 Gas Scattering Effects in the VPSEM
- •25.1.1 Why Doesn’t the EDS Collimator Exclude the Remote Skirt X-Rays?
- •25.2 What Can Be Done To Minimize gas Scattering in VPSEM?
- •25.2.2 Favorable Sample Characteristics
- •Particle Analysis
- •25.2.3 Unfavorable Sample Characteristics
- •References
- •26.1 Instrumentation
- •26.1.2 EDS Detector
- •26.1.3 Probe Current Measurement Device
- •Direct Measurement: Using a Faraday Cup and Picoammeter
- •A Faraday Cup
- •Electrically Isolated Stage
- •Indirect Measurement: Using a Calibration Spectrum
- •26.1.4 Conductive Coating
- •26.2 Sample Preparation
- •26.2.1 Standard Materials
- •26.2.2 Peak Reference Materials
- •26.3 Initial Set-Up
- •26.3.1 Calibrating the EDS Detector
- •Selecting a Pulse Process Time Constant
- •Energy Calibration
- •Quality Control
- •Sample Orientation
- •Detector Position
- •Probe Current
- •26.4 Collecting Data
- •26.4.1 Exploratory Spectrum
- •26.4.2 Experiment Optimization
- •26.4.3 Selecting Standards
- •26.4.4 Reference Spectra
- •26.4.5 Collecting Standards
- •26.4.6 Collecting Peak-Fitting References
- •26.5 Data Analysis
- •26.5.2 Quantification
- •26.6 Quality Check
- •Reference
- •27.2 Case Study: Aluminum Wire Failures in Residential Wiring
- •References
- •28: Cathodoluminescence
- •28.1 Origin
- •28.2 Measuring Cathodoluminescence
- •28.3 Applications of CL
- •28.3.1 Geology
- •Carbonado Diamond
- •Ancient Impact Zircons
- •28.3.2 Materials Science
- •Semiconductors
- •Lead-Acid Battery Plate Reactions
- •28.3.3 Organic Compounds
- •References
- •29.1.1 Single Crystals
- •29.1.2 Polycrystalline Materials
- •29.1.3 Conditions for Detecting Electron Channeling Contrast
- •Specimen Preparation
- •Instrument Conditions
- •29.2.1 Origin of EBSD Patterns
- •29.2.2 Cameras for EBSD Pattern Detection
- •29.2.3 EBSD Spatial Resolution
- •29.2.5 Steps in Typical EBSD Measurements
- •Sample Preparation for EBSD
- •Align Sample in the SEM
- •Check for EBSD Patterns
- •Adjust SEM and Select EBSD Map Parameters
- •Run the Automated Map
- •29.2.6 Display of the Acquired Data
- •29.2.7 Other Map Components
- •29.2.10 Application Example
- •Application of EBSD To Understand Meteorite Formation
- •29.2.11 Summary
- •Specimen Considerations
- •EBSD Detector
- •Selection of Candidate Crystallographic Phases
- •Microscope Operating Conditions and Pattern Optimization
- •Selection of EBSD Acquisition Parameters
- •Collect the Orientation Map
- •References
- •30.1 Introduction
- •30.2 Ion–Solid Interactions
- •30.3 Focused Ion Beam Systems
- •30.5 Preparation of Samples for SEM
- •30.5.1 Cross-Section Preparation
- •30.5.2 FIB Sample Preparation for 3D Techniques and Imaging
- •30.6 Summary
- •References
- •31: Ion Beam Microscopy
- •31.1 What Is So Useful About Ions?
- •31.2 Generating Ion Beams
- •31.3 Signal Generation in the HIM
- •31.5 Patterning with Ion Beams
- •31.7 Chemical Microanalysis with Ion Beams
- •References
- •Appendix
- •A Database of Electron–Solid Interactions
- •A Database of Electron–Solid Interactions
- •Introduction
- •Backscattered Electrons
- •Secondary Yields
- •Stopping Powers
- •X-ray Ionization Cross Sections
- •Conclusions
- •References
- •Index
- •Reference List
- •Index
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13.4 · Where to Learn More
developed by the Machine Learning Group at the University of Waikato in New Zealand (Hall et al. 2009). WEKA is a fullfeatured and very popular open source software suite written in Java for machine learning (ML) researchers. It provides an open, cross-platform workbench for common ML tasks such as data mining, feature selection, clustering, classification, and regression, going well beyond just image analysis. The Fiji plugin is a gateway into this large array of tools and provides a convenient interface for processing SEM images using a modern machine learning framework (7 http://imagej.net/
Trainable_Weka_Segmentation).
Some of the most widely used and powerful plugins in Fiji have been back-ported into ImageJ itself, and are available directly from the main application’s menu structure. An example of this is the Process menu option known as “Contrast Limited Adaptive Histogram Equalization,” or CLAHE (Zuiderveld 1994). First developed in 1994, this algorithm has been implemented in a wide variety of image processing tools. It is designed to amplify local contrast by performing histogram equalization on small subsets (tiles) within the source image, but to limit the allowed amplification to reduce the tendency to magnify the noise in relatively homogeneous patches. . Figure 13.3a shows a scanning electron micrograph of microfabricated features on silicon, acquired at 20 keV using an Everhart–Thornley detector. Because of slight misalignment of the raster with the linear features, Moiré contrast is evident in the image as bright edges on some features, and there are pure white and pure black horizontal lines that have been added to simulate contrast artifacts. These extreme limits of intensity preclude the usual brightness/contrast adjustments, but the CLAHE algorithm recovers invisible details without loss of information,
. Fig. 13.3b.
While it is possible that the ideal software tool for your project is available in Fiji itself (e.g., CLAHE) or in one of the many plugins loaded into Fiji by default (e.g., Trainable Weka Segmentation), it is much more likely that the tool you are looking for is not in the distribution you downloaded from the Fiji website. Only a small fraction of the plugins available to the user have been installed in the menu tree. A much larger collection awaits the user who is willing to explore the many optional Fiji update sites. The Updater window shown in . Fig. 13.1b has a “Manage update sites” button at the lower left. If you press this button you are presented with a list of optional plugin repositories, as shown in . Fig. 13.4a. When checked, these additional update sites will be accessed and used by the Updater to find new functionality to add into the base distribution. Some of the sites shown in . Fig. 13.4a only add one or two items to the Plugins menu, while others import
a much larger amount of supplemental code and capability. For example, the “Cookbook” site listed in . Fig. 13.4a adds a new top-level menu item to the Fiji main window, as shown in . Fig. 13.4b. This new menu contains example code to help new users follow along with a community- written tutorial introduction to ImageJ, available on the ImageJ website (7 http://imagej.net/Cookbook).
Occasionally a set of useful plugins will be written by a researcher or contributor who is unable or unwilling to make them available as an update site. The ImageJ website offers free hosting of update sites for any author of plugins, and organizations can run their own Fiji update sites if they wish. If these are not already a selectable option on the Manage update sites list (. Fig. 13.4a), the “Add update site” button allows the user to manually follow a third-party update site. As a last resort, plugins may also be manually installed into the Fiji plugins directory, but they will not be automatically updated so this is discouraged.
Thus, there are really four tiers of plugins across the ImageJ universe: (1) core ImageJ plugins that are bundled into the base ImageJ package (more than 1000 plugins in 2016); (2) core Fiji plugins, included by default in the “Batteries Included” Fiji distributions (more than 1000 additional plugins in 2016); (3) plugins available from additional update sites; and (4) plugins that must be located, downloaded, and installed manually. While this last category of plugins is the most likely to be buggy and poorly supported, any plugin written by a co-worker or officemate will often fall into this category, so the code may be highly specific to your task or your organization—don’t overlook these!
13.4\ Where to Learn More
Learning ImageJ or Fiji can be a daunting task for the beginner, and no attempt was made here to provide even a basic introduction to opening, exploring, manipulating, and saving SEM micrographs or X-ray data. However, there are many excellent resources for learning Fiji on the web, and the community offers several support channels for those who need additional help. Fiji itself has a built-in Help menu with links to the ImageJ and Fiji websites, newsgroups, online documentation, example code, developer tools, guidance documents, etc. The ImageJ Help page maintains links to the ImageJ Forum, Chat Room, and IRC channel as well as pointers to the ImageJ tag on Stack Overflow and Reddit, popular online locations for ImageJ and Fiji questions and answers. Finally, there is a synoptic search engine for many of the above resources at 7 http://
search.imagej.net.
192\ Chapter 13 · ImageJ and Fiji
. Fig. 13.3 Application of Fiji’s CLAHE processing to a lowcontrast SEM images a and the resulting enhanced image b. The images are 256 μm wide
13
a
b
References
. Fig. 13.4 a Fiji’s Manage Update Sites window, showing some of the many optional plugin repositories available for use. b A new top-level menu item called “Cookbook” imported from the Cookbook update site
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a
b
References
Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten IH (2009) The WEKA data mining software: an update. ACM SIGKDD Explor Newsl 11(1):10–18
Hiner M, Rueden C, Eliceiri K (2016) SCIFIO [Software]. 7 http://scif.io Pietzsch T, Preibisch S, Tomancak P et al (2012) ImgLib2—generic image
processing in Java. Bioinformatics 28(22):3009–3011, 7 http:// imagej.net/ImgLib2
Schindelin J, Arganda-Carreras I, Frise E et al (2012) “Fiji: an open-source platform for biological-image analysis”. Nat Methods 9(7):676–682, 7 https://fiji.sc (Note that Fiji is not spelled FIJI)
Schindelin J, Rueden CT, Hiner MC et al (2015) The imageJ ecosystem: an open platform for biomedical image analysis. Mol Reprod Dev 82(7–8):518–529
Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9(7):671–675
Zuiderveld K (1994) “Contrast limited adaptive histograph equalization.” graphic gems IV. Academic Press Professional, San Diego, pp 474–485