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How to install Imagej on Ubuntu 16.04

To install ImageJ on Ubuntu 16.04

ImageJ is a based image processing tool. It can be used for editing, analyzing , processing and to save images which range from 8- bit to 32 bit. It can also perform standard image editing tasks such as contrast manipulation, sharpening, smoothing, edge detection and median filtering. It supports are major image formats whiich includes TIFF, GIF, JPEG, BMP, DICOM, FITS and " raw" . It is capable of calculating area and pixel value statistics of user defined selections. Also, it can measure the distances and angles. Apart from this, it is also used for creating density histograms and line profile plots. This article helps you with the installation of ImageJ on Ubuntu 16.04

To install ImageJ

Before starting the installation, check for the universe repository is enabled. You can do it by inspecting ' /etc/apt/sources.list' with your favorite editor.

root@linuxhelp:~# vim /etc/apt/sources.list

If you had made any changes, run the following command to update your system.

root@linuxhelp:~# apt-get update
Hit http://security.ubuntu.com wily-security InRelease
Hit http://in.archive.ubuntu.com wily InRelease                        
Hit http://in.archive.ubuntu.com wily-updates InRelease                                     
Hit http://security.ubuntu.com wily-security/main Sources                                    
Ign http://us.archive.ubuntu.com trusty InRelease                                            
Hit http://in.archive.ubuntu.com wily-backports InRelease             
Hit http://security.ubuntu.com wily-security/restricted Sources                                
Get:1 http://us.archive.ubuntu.com trusty Release.gpg [933 B]         
Hit http://in.archive.ubuntu.com wily/main Sources                    
Hit http://security.ubuntu.com wily-security/universe Sources                       
Hit http://in.archive.ubuntu.com wily/restricted Sources                                 
Hit http://security.ubuntu.com wily-security/multiverse Sources                     
Get:2 http://us.archive.ubuntu.com trusty Release [58.5 kB]                         
Hit http://in.archive.ubuntu.com wily/universe Sources                        
Hit http://security.ubuntu.com wily-security/main amd64 Packages                             
Hit http://in.archive.ubuntu.com wily/multiverse Sources                                     
Hit http://security.ubuntu.com wily-security/restricted amd64 Packages     
Hit http://in.archive.ubuntu.com wily/main amd64 Packages                  
Hit http://security.ubuntu.com wily-security/universe amd64 Packages       
Hit http://in.archive.ubuntu.com wily/restricted amd64 Packages            
Hit http://security.ubuntu.com wily-security/multiverse amd64 Packages     
Hit http://in.archive.ubuntu.com wily/universe amd64 Packages                              
Hit http://security.ubuntu.com wily-security/main i386 Packages   
Get:3 http://us.archive.ubuntu.com trusty/main amd64 Packages [1,350 kB]                
Hit http://in.archive.ubuntu.com wily/multiverse amd64 Packages                                   
Hit http://security.ubuntu.com wily-security/restricted i386 Packages                             
Hit http://security.ubuntu.com wily-security/universe i386 Packages    
.
.
Get:7 http://us.archive.ubuntu.com trusty/main Translation-en [762 kB]                                     
Get:8 http://us.archive.ubuntu.com trusty/universe Translation-en [4,089 kB]                               
Ign http://us.archive.ubuntu.com trusty/main Translation-en_IN                                             
Ign http://us.archive.ubuntu.com trusty/universe Translation-en_IN                                         
Fetched 19.3 MB in 3min 12s (100 kB/s)                                                                     
Reading package lists... Done

Once the system is updated, install the ImageJ package by running the following command.

root@linuxhelp:~# apt-get install imagej
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  ca-certificates-java default-jre default-jre-headless fonts-dejavu-extra java-common libatk-wrapper-java
  libatk-wrapper-java-jni libgif4 libsctp1 lksctp-tools openjdk-7-jre openjdk-7-jre-headless tzdata
  tzdata-java
Suggested packages:
  equivs icedtea-7-plugin icedtea-7-jre-jamvm sun-java6-fonts fonts-ipafont-gothic fonts-ipafont-mincho
  ttf-wqy-microhei ttf-wqy-zenhei fonts-indic
Recommended packages:
  libgnome-2-0
The following NEW packages will be installed:
  ca-certificates-java default-jre default-jre-headless fonts-dejavu-extra imagej java-common
  libatk-wrapper-java libatk-wrapper-java-jni libgif4 libsctp1 lksctp-tools openjdk-7-jre
  openjdk-7-jre-headless tzdata-java
The following packages will be upgraded:
  tzdata
1 upgraded, 14 newly installed, 0 to remove and 253 not upgraded.
Need to get 43.7 MB of archives.
After this operation, 66.7 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://in.archive.ubuntu.com/ubuntu/ wily/main libgif4 amd64 4.1.6-11 [28.6 kB]
Get:2 http://in.archive.ubuntu.com/ubuntu/ wily/main libsctp1 amd64 1.0.16+dfsg-2 [8,414 B]
Get:3 http://in.archive.ubuntu.com/ubuntu/ wily/main java-common all 0.52 [131 kB]
Get:4 http://in.archive.ubuntu.com/ubuntu/ wily/main default-jre-headless amd64 2:1.7-52 [4,086 B]

.
.
Processing triggers for libc-bin (2.21-0ubuntu4) ...
Processing triggers for ca-certificates (20150426ubuntu1) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed  done.
Running hooks in /etc/ca-certificates/update.d...
done.
done.

ImageJ is now installed. Type the package name in the terminal and hit enter to open the package.


Tag : Image resizer Ubuntu ImageJ
FAQ
Q
How do I quantify a gel with ImageJ?
A
Electrophoretic gels such as Western blots can be quantified easily with ImageJ using the Analyze▷Gels▷ commands, as described on this video tutorial. Further details are explained on the ImageJ User Guide.
Please read the Guide's section Using Scanners in Densitometry before performing your quantifications.
Q
What is this headless mode and what do I need it for?
A
The term headless refers to running ImageJ without a graphical desktop, e.g. on a cluster. See the Headless page for more information.
Q
What is this headless mode and what do I need it for?
A
The term headless refers to running ImageJ without a graphical desktop, e.g. on a cluster. See the Headless page for more information.
Q
Can I convert a large stack into .avi, .gif, QuickTime without loading it?
A
With ImageJ 1.39k and later, you can frame-by-frame convert a large TIFF by opening stack it using File>Import>TIFF Virtual Stack and saving it using File>Save As>AVI, File>Save As>Gif (animated GIF) or File>Save As>QuickTime Movie. Set the frame rate in the Image>Stacks>Animation Options dialog.
Q
I want to run ImageJ on a cluster, by executing batch macros. To do that, I use ssh to log on, but ImageJ throws an exception that it cannot create a Menu in headless mode. What to do?
A
There are at least two methods:
Install a virtual framebuffer (Xvfb) if you are on Unix. On a Mac, this will not necessarily help.
Use Fiji's headless mode (available via the command-line option –headless.