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中国体视学与图像分析 2012 年 第 17 卷 第 4 期
CHINESE JOURNAL OF STEREOLOGY AND IMAGE ANALYSIS Vol． 17 No． 4 Dec． 2012 301

文章编号： 1007 － 1482 （ 2012） 04 － 0301 － 0312 ·图像处理分析方法·

A framework for image processing，

analysis and visualization of materials
microstructures using ImageJ package
Asad Ullah1，2 ， Guoquan Liu1，3 ， Hao Wang1 ， Dil Faraz Khan1 ， Matiullah Khan1

（ 1. School of Materials Science and Engineering，University of Science and Technology Beijing，

Beijing 100083，China； 2. Department of Mathematics，Karakoram International University Gilgit-Baltistan，
Gilgit 15100，Pakistan； 3. State Key Laboratory for Advanced Metals and Materials，University of
Science and Technology Beijing，Beijing 100083，China）

Abstract： Digital image processing，segmentation and analysis of microstructural images are crucial to ob-
tain three dimensional （ 3D） information about the features present in microstructure such as particles or
grains． There are several commercial as well as public domain packages availible for processing and analy-
sis of images； “ImageJ”is one of them whose wide adoption，long existence and extensible plugin style
has made it a tool of choice for scientists from a broad range of disciplines． It contains almost all of the
basic and latest functionalities required to process，segment，reconstruct and visualize materials micro-
structural images along with analysis tools （ for instance ‘Particle Analyzer’，‘3D object counter’，‘3D
Roi Manager’and so on） for sophisticated statistical processing of groups of particles． Although it is very
popular and is considered to be an useful and efficient open source image processing and analysis software
in biomedical research fields，a little is known about it in materials science sector． In this article we intro-
duce ‘ImageJ’briefly to materials science community （ particularly those professionals who have no expe-
rience of image processing and analysis） and propose a general frame work to process，segment，analyze
and visualize microstructural serial section images in 3D by using it．
Key words： material stereology； microstructure； serial section images； imageJ； image segmentation； im-
age analysis

CLC number： TG113. 1； TP391 Document code： A

收稿日期： 2012-11-20
基金项目： 国家自然科学基金（ 51071019，
50901008，
50871017） 。
作者简介： Asad Ullah（ 1983 － ） ，男，Gilgit-Baltistan，Pakistan。研究方向： 数学和计算材料科学。
通信作者： 刘国权，教授。E-mail： g． liu@ustb． edu． cn
302 中国体视学与图像分析 2012 年 第 17 卷 第4 期

应用 ImageJ 程序包进行材料显微组织图像处理、分析和可视化的一种框架

Asad Ullah1，2 ， 刘国权1，3，， 王 1 1

浩 ， Dil Faraz Khan ， Matiullah Khan
1

（ 1. 北京科技大学 材料科学与工程学院，北京 100083； 2. Department of Mathematics，

Karakoram International University Gilgit-Baltistan，Gilgit 15100，Pakistan） ；
3. 北京科技大学 新金属材料国家重点实验室，北京 100083）

摘 要： 显微组织图像 （ 例如胞、粒子与晶粒等 ） 的数字图像处理、分割和分析，对于获取显微组织

特征的三维信息非常重要。已有数种商用和共享程序包可以用于图像的处理和分析。“ImageJ”即
其中之一，其长期广泛采用及其可扩展插件形式已使其成为许多不同应用领域科学家选用的工具 。
它包含了处理、分割、重建和可视化材料显微结构所需要的几乎所有基本的和最新的功能以及图像
分析工具（ 例如‘Particle Analyzer’，‘3D object counter’，‘3D Roi Manager’） ，以用于成组粒子的复
杂统计处理。虽然它在生物医学研究领域很受欢迎，被认为是一种有用的和有效的开放源码的图
像处理与分析软件，但是在材料科学领域对其所知甚少。 面向材料学界，本文尤其是那些没有图
像处理和分析经验的材料科学与工程专业人员 ，在简要介绍 ImageJ 的基础上，提出了将其应用于在
三维空间中处理、分割和分析显微组织结构连续切片图像的一个通用框架 。
关键词： 材料体视学； 显微组织； 系列截面图像； ImageJ； 图像分割； 图像分析

transparent and everyone can know the full details of al-

0 Introduction
The contribution of technological advances in the
field of materials science and engineering is well recog-
nized． Three dimensional microstructural image pro-
cessing and analysis is a key step towards materials
characterization in which many researchers and materi-
als scientists have used technological advances （ latest
computer vision and other image processing approa-
ches） to good advantage． There are several open source
［1］ ［2］
（ for example，Vaa3D ，CellProfiler ，ImageSurf-
［3］ ［4］ ［5］
er BioImageXD ， Reconstruct ， IMOD
others） and commercial （ for example，Amira，Volocity
and Imaris） software packages for the processing and a-
nalysis of images，a complete review of imaging soft-
ware tools can be found in ［7］． Most of the commer-
cial image processing and analysis softwares are often
expensive and one of their important drawbacks is hid-
ing the details of the implemented algorithms． Con-
versely， in open-source softwares these details are
gorithms，which is very useful to decide which algo-
rithm is better suited according to the needs of user．
ImageJ，an open-source Java-based image processing
and analysis software created by Wayne Rasband at the
US National Institutes of Health （ NIH） ［8 － 9］ is a cost-
effective alternative for processing and analysis of mi-
crostructural images． ImageJ is unique among all the
open source softwares because it is not only in the pub-
lic domain，but also runs on any operating system． It
has a particularly outstanding application programming
interface （ API） ． The reason for its attractiveness is be-
［6］
and cause of its ease of use，and it can perform a full set
of imaging manipulations． According to a current
［10］
study ，the ImageJ website［11］ has ～ 7000 visitors a
day and a huge and knowledgeable community compri-
sing of ～ 1900 members are subscribed to the ImageJ
mailing list as of May 2012． According to a PubMed
search conducted in May 2012，there have been found
over 20 000 papers which used imageJ［10］． A screen
shot of the main window of imageJ is shown in fig． 1．
2012 年 第 17 卷 第4 期 Asad Ullah et al： A framework for image processing，analysis and
visualization of materials microstructures using ImageJ package
Fig． 1 Screen shot of imageJ's main window
ImageJ can read most of the common and impor-
tant image formats including BMP，TIFF，JPEG，GIF，
DICOM，FITS，and PNG，RAW and many other for-
mats． It can display，save，edit，print，process and
analyze 8-bit grayscale and color，16-bit integer and
32-bit floating point images． It supports all types of
common image manipulations including whole images，
volumes，specific image regions and individual pixels．
The concept of volume in ImageJ is actually the stack of
a sequence of images that share a single window． It can
perform many image processing，segmentation and a-
nalysis operations，for instance，logical and arithmeti-
cal operations between images，contrast manipulation，
convolution， Fourier analysis， distance transforma-
tions，sharpening，smoothing，edge detection，morpho-
logical operations，median filtering，watershed segmen-
tation，particle analysis and many other advanced oper-
ations． It performs image processing and analysis tasks
using filters，these filters are written as plugins． Due to
its open source nature，it is extensible via its Java plu-
gins and recordable macros； user community can devel-
op the plugins according to their needs and add them to
ImageJ to extend its functionality． According to a re-
cent study［10］，ImageJ has more than 500 plugins to
perform different operations on images． A full review of
the evolution of ImageJ and its role in image processing
and analysis is well beyond the scope of this article，
but one can refer to ［8 － 10］for an excellent overview
about its all aspects．
Because of its popularity in biomedical and biolog-
ical research fields，ImageJ has emerged as increasing-
ly used image processing and analysis software in di-
verse applications ranging from astronomy，soil sciences
and climate sciences，to crystallography and materials
science． As for as materials science research sector is
concerned，still a little is known about it． To the best
303
of our knowledge，there are few studies in materials
science which used imageJ for processing and analysis
of microstructural images，for instance ［12 － 16］，but
most of them only used a specific plugin for a specific
task and used other commercial softwares for the rest of
processing． This seems to be the result of lack of
awareness about the functionalities and plugins of im-
ageJ and also lack of a strong collaboration between bi-
ologists and materials science researchers； ultimately
there exists a communication gap． Therefore，we felt it
is necessary to put an effort towards reducing this com-
munication gap to some extent by proposing a general
framework to process，segment，analyze，reconstruct
and visualize materials microstructural images in three
dimensions by using imageJ． As a case study，this arti-
cle used optical microscopy serial section images of pure
iron．
1. The framework
In order to convert the experimental serial section
images into three dimensional volume datasets for fur-
ther characterization and visualization purposes，several
processing steps are required． These processing steps
include， importing images into imageJ， setting the
scale，registering （ aligning） ，selecting the region of
interest （ ROI） and cropping，segmenting particles or
grains in images，making the image stack isotropic，an-
alyzing grains or particles and finally visualizing the
particles to study the morphology and other shape fac-
tors． The details of each of these steps are given below．
1． 1 Importing images into imageJ and setting the
measurement scale
ImageJ can read many image formats as described
in section 1． To import the images into imageJ，the im-
 304 中国体视学与图像分析
ages have to be placed into a folder in a proper
sequence according to the acquisition order． These im-
ages can be accessed by browsing through File ＞ import
command from imageJ menu． Thus，the sequence of
images is imported into imageJ in form of a scrollable
stack displayed in a single window． In this study，we
imported 100 image sections which formed our stack，
as shown in fig． 2．
To set the measurement scale，the scale bar on the
original microscope images can be used，by selecting
the ‘Straight line’tool from menu bar and drawing a
（ a） Showing the position of scroll bar at 25 th image section； （ b） A different orientation view depicting the stack hierarchy of imageJ．
Fig. 2
1． 2 Image registration
The rotational and translational shifts produced in
images during experiment due to the manual placing of
sample in microscope stage or some other reasons can
be corrected in imageJ by manual and automatic
means． There are many imageJ plugins available for
image registration，we used two of them in this study
namely ‘Align3 _ TP ’ ［17］
and ‘Stackreg ’ ． The ［18］
‘Align3_TP’plugin can be located from imageJ menu
bar by selecting Plugins ＞ Align Stacks ＞ Align3 _ TP
and Stackreg can be located by selecting Plugins ＞
Stacks ＞ Stackreg． ‘Align3_TP’plugin allows the user
to register two images （ or two image stacks） ，by suc-
cessively aligning two dimensional （ 2D） sections． We
used it for an initial alignment of images by overlaying
two consecutive images and manually rotating and
2012 年 第 17 卷 第4 期
line the length of the scale bar． This line length is giv-
en in pixels． Then Analyze ＞ set scale command is used
to fill the information about the distance （ the value of
scale bar） in ‘Known distance’field and desired unit
in ‘Unit of length ’ field，the ‘Distance in pixels ’
field is filled automatically due to the drawing of line on
scale bar． In our case，we have the ‘known distance’
（ value of scale bar） as 100 μm （ as shown in fig． 2）
and ‘Distance in pixels’as 126，this sets the in-section
resolution of our images which is 0． 974 μm． ImageJ
uses this scale for all the measurements on images．
Stack of imported images
translating the second image with respect to the first，
which reduced some major rotational and translational
shifts． However，this process cannot completely align
the stack because of the lack of sub-pixel accuracy．
The sub-pixel accuracy can be achieved by using
‘Stackreg’plugin． The algorithm used in this plugin
provides the recursive alignment of stacks where each
image is used as the template with respect to which the
next image is aligned，based on a coarse-to-fine itera-
tive strategy known as“pyramid approach”． For exam-
ple，first image is used as the template for second im-
age and after alignment with first one this resulting im-
age will be used as the template for third image and so
on． Thus，the alignment process is finished only when
the images are perfectly aligned on each other． Com-
plete details of the algorithm can be found in ［18］．
When the plugin is launched，the current slice acts as
2012 年 第 17 卷 第4 期 Asad Ullah et al： A framework for image processing，analysis and
visualization of materials microstructures using ImageJ package
a global anchor． In this study，we used the first image
of our stack as global anchor and thus got the entire im-
age stack completely registered with sub-pixel accuracy．
The stack of registered images is shown in fig． 3（ d） ．
1． 3 Image cleanup and segmentation
Image segmentation is an important step towards
analysis of grains． Its main objective is to separate the
objects of interest from background and from each other
as well． Several automatic and manual image segmenta-
tion methods are available in the literature，such as
thresholding，region growing，watershed segmentation，
edge detection and so on． The selection of a specific
method depends on the imaging condition under which
the image is acquired． However，a suitable segmenta-
tion method must be applied for each type of image ac-
quired． An overview of image segmentation methods
can be found in ［19 － 20］．
Before starting the segmentation process，the re-
gion of interest （ ROI） has to be selected in the image
stack and cropped，this can be done by selecting the
‘rectangular tool’button from below the menu bar to
outline the desired area and cropped by using Image ＞
crop command from menu bar． After cropping the ROI，
the boundaries of objects （ grains / particles） have to be
identified in each 2D image． This is accomplished by
applying a threshold using Image ＞ Adjust ＞ Thresh-
old command，provided that the objects have homoge-
neous pixel values and there is a significant difference
between the pixel values of objects and background．
Otherwise，the image background should be subtracted
by using Process ＞ Subtract Background command be-
fore thresholding． There are different options available
in imageJ for thresholding 2D images or 3D stacks （ vol-
umetric datasets ） including automatic （ by selecting
different algorithms，e． g． Huang，Isodata，Li，Otsu，
MaxEntroppy，Yen and so on） and manual （ by selec-
ting an interval of values manually） thresholding． It is
often not the case that the objects are thresholded in a
satisfactory way． Mathematical morphology provides
some sophisticated tools for morphological operations
305
such as dilation，erosion and Euclidean distance map，
which may improve the thresholded images，but a man-
ual segmentation is necessary to completely clean the
remaining artifacts．
Here，we have cropped an area of 300 × 270 μm
（ note that imageJ can also handle massive datasets but
here we selected a small ROI from our dataset for dem-
onstration purposes） from our image stack and applied
a brightness threshold to convert the stack into a binary
volumetric data set in a way that each pixel belonging to
the interior of grain is set to white，while each belong-
ing to the boundaries is set to black． However，after
thresholding，the images were not cleaned properly and
there remained some spots and other artifacts． To re-
move the spots，we have applied some morphological
operations e． g． morphological opening，in which an e-
rosion operation is followed by a dilatation that removed
some small spots in the background． These commands
can be reached via Process ＞ Binary ＞ Dilate and
Process ＞ Binary ＞ Erode from the menu． Other re-
maining artifacts are corrected manually． It is also
usual that in case of space-filling grains，some grain
boundaries left unfilled within the image sections after
thresholding （ fig． 3 （ a） ） and in case of particles dis-
persed in matrix phase，some particles may overlap．
This is actually the result of low contrast between parti-
cle-particle contacts． There are several options in im-
ageJ to address these issues，but for such type of prob-
lems a 3D watershed segmentation algorithm is always
considered to be a best choice． It does not only correct
these boundary problems but also labels each 3D parti-
cle with a unique identifier，which is very useful for
analysis of particles． In some recent studies it was ap-
plied to overcome similar problems［21 － 22］．
ImageJ have some plugins to implement 3D water-
shed segmentation on image stacks，but unfortunately
its results are not satisfactory． Instead，some alternative
methods can be applied to fill these gaps in grain
boundary interfaces． One way is to apply a binary wa-
tershed algorithm （ note that this algorithm works only
on 2D binary images） on the stack of images by selec-
ting Process ＞ Binary ＞ Watershed command from
306 中国体视学与图像分析 2012 年 第 17 卷 第4 期

menu，it automatically fills the boundary gaps or sepa-
rates the overlapping particles in each 2D image，and
this method works best for smooth convex objects that
do not overlap too much． The second method is to cre-
ate an Euclidean Distance Map （ EDM） of each 2D im-
age in the stack and then find the local maxima by se-
lecting Process ＞ Binary ＞ Distance Map and then
Process ＞ Find Maxima． Here，we used the second
method to fill the grain boundary gaps exist in each 2D
image by selecting a suitable noise tolerance． Actually
the‘Find Maxima’command finds the local maxima in
an image and creates one segmented particle per maxi-
mum upon selecting ‘Segmented Particles’from drop
down menu of ‘Output type’as shown in fig． 3（ b） ＆
（ c） ． To apply it on whole image stack the‘FindStack-
Maxima’macro was used． Thus，it automatically filled
the missing gaps in each image of our stack． Although
these plugins operate in only 2D on a section by section
basis，but is far better than manually tracing the grain
boundaries on each 2D image，which is time consu-
ming． Fig． 3 （ d） shows the final stack of thresholded
and cleaned images，in which the images are perfectly
aligned on each other with sub-pixel accuracy．
The next step in the segmentation process is labe-
ling of objects for quantitative analysis． There exist some
commands and plugins in imageJ for labeling of parti-
cles． The Analyze ＞ Analyze Particles command can be
used to label particles in 2D，it can be applied to 3D
stacks but it labels particles independently in each 2D
image section so that the same particle gets different
identifiers in different sections． This problem can be
avoided by applying a 3D labeling method． In this in-
stance，the ‘3D object counter’plugin［23］ is the best
choice for 3D labeling of particles． It first applies a
threshold to image stack and labels each particle in 3D，
and also computes geometrical measures． Once installed
in plugins folder，this plugin can be reached via Plugins
＞ 3D Object counter． The output of‘3D object counter’
applied to our images stack is shown in fig． 4．

（ a） Showing the gaps exist in grain boundaries after thresholding； （ b） Showing the euclidean distance map of image
followed by‘find maxima’operation． The‘ + ’marks inside the image depict the local maxima of each grain； （ c）
Shows the result of‘find maxima’operation，which filled the gaps in grain boundaries； （ d） Shows segmented
and perfectly aligned （ with sub-pixel accuracy） image stack．
Fig． 3 A step by step process of image segmentation and cleanup
2012 年 第 17 卷 第4 期 Asad Ullah et al： A framework for image processing，analysis and 307
visualization of materials microstructures using ImageJ package

Fig． 4 The output of‘3D Object Counter’plugin showing 3D segmented and labeled grains． Labels are
shown as unique colors as well as integers （ see the integers inside small rounded rectangles on the
upper left portion of the screen shot） ． The Log window shows the count of grains and the results
window shows geometrical measurements．

mand twice． The other way is using the plugins ‘Make

2 Image calibration and scaling
Before starting measurements the image must be
calibrated in 3D，which can be done by entering the
pixel width，height and depth using image ＞ Properties
command． It is often the case that the Z spacing is gen-
erally much larger than the X － Y spacing and hence
the voxels are taller along Z-direction as compared to X
and Y，this is due to the acquisition systems． These
anisotropic voxel dimensions ultimately form an aniso-
tropic image stack． Although these anisotropic voxel di-
mensions do not affect the measurement process，how-
ever，isotropic voxel dimensions are usually preferred
for 3D analysis and especially for effective high-resolu-
tion reconstruction and visualization．
ImageJ have several options to rescale the image
stacks and make them isotropic． One way is to reslice
the data by using Image ＞ Stacks ＞ Reslice［/］ com-
Isotropic’developed by Julian Cooper or ‘TransformJ’
developed by Erik Meijering［24］． In this study，‘Trans-
formJ’plugin is used to scale the stack anisotropically
and selected the cubic convolution interpolation method
to get the isotropic voxel dimensions． Once installed，
this plugin can be reached via Plugins ＞ TransformJ
＞ TransformJ Scale from the menu bar．
3 Quantitative analysis of 3D grains
The overarching aim of image analysis is the quan-
titative measurement of 3D grains or particles in image
stack，preferably in an automatic way． Once the grains
have been segmented and labeled，and images have
been calibrated in 3D，the quantitative analysis can be
performed on each individual grain． ImageJ have sever-
al plugins to perform geometrical and intensity based
measurements on 3D grains for example the basic 3D
 308 中国体视学与图像分析 2012 年 第 17 卷 第4 期

［23］
analysis plugins include ‘3D object counter ’ and
［25］
‘3D Roi Manager’ ． In this study，we firstly used
‘3D object counter ’ plugin to label each 3D grain
（ this plugin also computes geometrical measures as
shown in fig． 4） and then used ‘3D Roi Manager’to
get the geometrical and intensity measurements．
As the particle size and surface area are key char-
acteristics which control many properties of materials
for example flowability，agglomeration，dusting tenden-
cy and other mechanical properties （ Hall-Petch effect）
and so on． The ‘3D Roi Manager’can compute these
characteristics and many other geometrical measures in-
cluding ferret diameter，sphericity or compacity （ ratio
between volume and surface） and ellipsoid fitting； the
minimum，maximum and mean distance from the center
of the particle to its boundary，etc． The intensity meas-
ures include min，max，mean，integrated density，etc．
It can also compute the 3D distance measurements from
one particle to others （ for example，the distance from
centre to centre，border to border，border to centre，
eccentricity，radial distance） ，3D angles between three
particles and 3D colocalization and contact surface． A
screen shot of these measurements on our image stack is
shown in fig． 5． According to the measurements，there
are a total of 273 grains in our image stack． However，
for an unbiased quantitative analysis it is better to re-
move the grains which touching the border of the sam-
ple，this can be done in ‘3D object counter’． Thus，
after removing the outside grains，a total of 91 unbiased
grains left in our sample with the largest grain having
volume 229 201． 41 μm3 ，ferret diameter 120． 875 μm
and the smallest grain having volume 3404． 36 μm3 and
ferret diameter 25． 445 μm． Both of these largest and
smallest grains are shown in fig． 7．

Fig． 5 The upper right window is the‘3D Roi Manager’showing a list which contains ID's of grains which are added
via segmented image of‘3D Object Counter’by using‘Add Image’button （ can be seen clearly） ． The upper
left window is the segmented image sack which is added for measurements． The windows‘3D Measure’，‘3D
Quantify’and‘3D Distance’show the geometrical，intensity and distance measurement results respectively．
2012 年 第 17 卷 第4 期 Asad Ullah et al： A framework for image processing，analysis and 309
visualization of materials microstructures using ImageJ package

Besides these basic plugins，there available many
other plugins which can be used for quantitative analy-
sis of grains or particles． For instance，the ‘Particle
［26］
Analyser’in ‘BoneJ’ plugin can be used to meas-
ure particles in a 3D binary image stack． This plugin
was particularly developed for bone image analysis，es-
pecially to study ‘osteocyte （ star shaped cells） lacu-
nae’in bones，but it can be used to study any porous
media． Like‘3D object counter’and‘3D Roi Manag-
er’，it also labels unique particles and analyze each
particle separately． It can compute many important
quantities for each individual particle including vol-
ume，surface area，Euler characteristic，local thick-
ness，moments of inertia，Ferret diameter，number of
topological holes （ handles） in the particle，number of
enclosed cavities in the particle and coordinates of cen-
troid of particles． It calculates the surface area by first
creating a surface mesh of each particle by using the
well known marching cubes algorithm［27］ and then
adding the areas of triangles making up the mesh． The
volume enclosed by surface mesh and the best fit ellip-
soids to the mesh of each particle can also be computed
by using it． Fig． 6 shows the ellipsoids fitted to each
grain's surface mesh．

Fig． 6 Results of‘Particle Analyser’． The upper left window shows the surface renderings of each grain during
quantification process，while the ellipsoids fitted to each grain are also visible clearly． The upper right
window shows the segmented 3D grains in the image stack． The Results window shows the measurement
results． Log window shows warnings about grains which could not be rendered due to small size．

［28］
Another useful plugin is‘3D Convex Hull’ ，it
calculates the 3D shape descriptors for example 3D so-
lidity and 3D Convexity based on a convex hull con-
structed from the image stack． Other numerous plugins
are freely available online which can cater the needs of
materials science researchers．
4 3D visualization of microstructures
To better understand the data it is necessary to vis-
ualize it in 3D，which can be helpful to determine ap-
propriate analysis methods or parameters． ImageJ is
considered to be a popular tool to analyze and visualize
massive datasets of microscopic images． It provides
practical solutions for memory management and displa-
ying large datasets without unrealistic hardware require-
ments［29］．
Volumes can be visualized by either volume ren-
dering or surface rendering． Volume rendering can be
310 中国体视学与图像分析 2012 年 第 17 卷 第4 期

defined as the rendering of all the volume data by spec-
ifying color and opacity of each voxel and surface ren-
dering is the rendering of the iso-surface of the region
of interest （ ROI） from volume data． There available
two important and powerful imageJ plugins ‘Volume
Viewer’and ‘ImageJ 3D Viewer’for 3D visualization
and manipulation of massive datasets． The ‘Volume
Viewer’plugin can be used for more complex volume
visualizations in which one can slice in any direction
inside the volume． The hardware accelerated ‘ImageJ
［30］
3D Viewer’plugin can be used to visualize the data
as volume，orthogonal slices and surfaces at the same
time． There exist several ways to implement volume
renderings，such as ray-casting［31］ and texture map-
ping． ‘ImageJ 3D Viewer’uses 2D texture mapping
method for volume rendering，that ’s why it is user
friendly and does not need dedicated workstations，
rather it can be run on common laptops． For surface
rendering，it uses a variant of marching cubes algo-
rithm［32］ which is a useful algorithm to preserve the to-
pology of particles or grains during rendering．
In this article，we used ‘ImageJ 3D Viewer’plu-
gin for both volume and surface renderings． As before
visualization，the brightness and contrast of the image
stack must be adjusted for an improved visualization．
We adjusted the brightness and contrast by using the
command Process ＞ Enhance Contrast，in which there
are several options but the ‘Normalize’option is best
among all，which allows all the image sections in the
stack to have almost the same brightness and contrast．
The 3D volume and surface renderings of our image
stack are shown in fig． 7． By using ‘ImageJ 3D Vie-
wer’one can also render each individual grain from
image stack for visualization and the rendered dataset
can be animated and saved as movies． We rendered
here the largest and the smallest grains in our dataset，
as shown in fig． 7．

（ a） Surface rendered microstructure formed from 100 sections，composing a volume of 300 × 270 × 170 μm3 ，containing
273 grains； （ b） Surface rendered microstructure containing 91 grains，border touching grains are removed for unbiased
quantitative analysis； （ c） The largest and smallest grains in the system； （ d） Volume rendered microstructure．
Fig． 7 Different views of surface rendered and volume rendered microstructures
2012 年 第 17 卷 第4 期 Asad Ullah et al： A framework for image processing，analysis and
visualization of materials microstructures using ImageJ package
5 Discussion and conclusions
Although there are available hundreds of imageJ
plugins for a full set of image manipulation and visual-
ization，we tried here to report the best from each cate-
gory that can do the best job according to the situation
and image conditions，and materials microstructural im-
ages remained our main foci in this study． Specially，
our main target in this study was thosematerials science
and engineering professionals who have no experience
in image processing and analysis． As image processing
and analysis tasks can be performed by using a variety
of computer languages for example lower level compiled
languages such as FORTRAN and C + + ，and scrip-
ting languages such as MATLAB TM and IDL TM ． Al-
though the scripting languages are tend to be easier
than compiled languages but for a novice person it is a
very difficult and time consuming task to first learn pro-
gramming and then apply it to solve problems in the
relevant field． Instead，most of the researchers prefer
to look for cost-effective and easy to use softwares
which can cater their needs in an optimal way． In this
instance，imageJ，due to its ease of use and open
source nature，is a best choice for materials science
and engineering professionals． It allows to do a full set
of imaging manipulations which can hardly be found in
an open-source software． As it is discussed above that
imageJ has hundreds of plugins to perform image pro-
cessing，analysis and visualization tasks so to choose
best plugin for the right job is very important and at the
same time very difficult also． In this article we mainly
focused on this issue and tried to resolve it by selecting
best plugins from each category to do the right job and
practically demonstrated the importance of each plugin
by applying it to the optical microscopic serial sections
of real microstructures．
Finally，it is worth introducing here a variant of
imageJ namely ‘Fiji’，Fiji［33］ is an open-source distri-
bution of imageJ in which the plugins are organized cat-
egory-wise in a well mannered way． It enhances imageJ
by updating the infrastructure of the program，using
311
modern software engineering practices． It is easy to use
due to its organization of plugins． One can use any of
imageJ or Fiji for full image manipulation and visualiza-
tion．
To sum up，we introduced imageJ briefly to mate-
rials science community and outlined a general frame-
work to process，segment，analyze，reconstruct and
visualize materials microstructural images in three di-
mensions by using it． We hope that this framework will
be helpful to materials science and engineering re-
searchers，especially those professionals who do not
have any experience in image processing and analysis．
Acknowledgements
The authors gratefully acknowledge the financial
support from National Natural Science Foundation of
China （ 51071019，50901008 and 50871017） ．
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