Download ImageJ for Mac OS X from the Download page. The ZIP file you download (Image1.xx.zip) should automatically expand to Image.app, which is normally copied into the Applications folder. Mac OS X Download ImageJ bundled with Java 1.8.0172 (may need to work around Path Randomization). Also available as an application that uses Apple's version of Java 6 (does not work on High Sierra). Linux Download ImageJ bundled with Java 1.8.0112 (82MB). ImageJ 10.2 for Mac can be downloaded from our software library for free. The size of the latest setup package available is 5.4 MB. The ImageJ installer is commonly called ImageJ143.zip, ImageJ144.zip or imagej146.zip etc. Our built-in antivirus scanned this Mac download and rated it as 100% safe. Download the.dmg package from the Downloads page, and then double-click it to open it. Create a folder under /Applications/, such as /Applications/Fiji Drag the 3 items (Fiji.app, and the plugins and macros symlinks) into the /Applications/Fiji folder.
About![]()
ImageJ is an open source java-based image processing program designed for analysis of various microscope data.ImageJ is powerful in that it allows you to write your own simple plugins as .java files - many plugins have been written (see list) - most of these .jar files you can simply drag into the 'plugins' directory. Due to its open source nature, many people have also 'built' or taken from ImageJ, including the program 'CellProfiler' (Carpenter et al 2006 [1]) and others listed here.
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InstallationImageJ
You can download the latest stable version of ImageJ here and installation is as simple as running the .exe (on Windows) or copying the ImageJ folder into the Applications directory (on Mac).
Fiji... (same thing, but with more plugins pre-installed)
Fiji is basically ImageJ with a large number of plugins and segmentation tools already built in. How to use winebottler. You can download the latest version of Fiji from here. If you intend to do lots of image segmentation, I recommend you install 'Figi' instead of ImageJ - it behaves exactly the same as ImageJ, but can save you the effort of needing to install these extra plugins yourself.
Tricks and Examples
In this section I list out a few little tricks and example application of ImageJ/Fiji.
Creating a Macro to Batch Process a Directory
One of ImageJ's most useful features is the ability to record, write and run Macros. Macros are helpful whenever you find yourself applying the same actions over and over again. What can be especially useful is to record a macro and then set it up in such a way that you can batch process a bunch of images in one directory, and output with the same filenames to a different directory. There are instructions on how to record and apply instructions are here: How to apply a common operation to a complete directory. The basic steps are:
At this stage your Macro should look like this:
At this stage you'll notice that running the Macro on any image overwrites exactly the same file ('output.tif'). What you need to do next is adapt your '.ijm' macro file to automatically process a whole directory of files and save each to a different file name. To do this modify your code so it looks like this:
Running this code should process all files in your 'in' directory into the 'out' directory you specified (with a matching file name). To run this Macro at a later time open Fiji then select Plugins > Marcos > Run. then select your .ijm file.. or alternatively you can execute a Macro from the command line. On Mac OSX the command will look like this:
Nucleus Separation Example
In light microscopy, biologists often stain the DNA in the cell nuclei with DAPI to help see the Nucleus. On the Fiji website there is a very nice article on how to count and isolate these nucleus. The full article is here: Nuclei Watershed Separation, and below are the key points from this article with a few optional steps added courtesy of Alex Perez:
Once you've done this a few times and are happy with all your parameters and results you can then create a Macro to apply these steps automatically to a series of files. Following the instructions in the section above 'Creating a Macro to Batch Process a Directory', you can record a macro, then you'll want to save the macro as 'Macro_DAPI_Watershed.ijm' and modify the code to look like this:
Running this code should process all files in your 'in' directory into the 'out' directory you specified. To run this Macro open Fiji then select Plugins > Marcos > Run. then select your .ijm file.. or alternatively you can execute a Macro from the command line. On Mac OSX the command will look like this: Extrack dmg dvd on windows.
In Alex's project this came in useful because he wanted to convert a 3D dataset from IMOD in MRC file format. While Fiji can open MRC files, not all its functions apply over 3D and it can't save MRC, so instead Alex used scripts to save the MRC to tifs, run the Image J macro, then joined all these new tifs back into a new MRC. In the final steps he then generate IMOD contours and surface meshes over the various boundaries. The unix commands for this were:
Particle Analysis Example
An old colleague from Australia had an interesting problem where he wanted to mark up alveoli inside the lungs of a developing mouse embryo imaged with a light microscope. Apparently there are tens of these things, and many on top of each other; therefore making it difficult for automatic segmentation.
Instead I suggested marking them up manually by drawing circles, and using the following steps:
To reopen this you simple start ImageJ, then open the image file, then open the 'RoiSet' .zip file. It also looks like you might also be able to batch process a number of these using: Plugins >> Analyze >> Batch Measure, but I haven't figured this out yet.
Turn an Image Sequence into an AVI Movie
Although ImageJ reads and writes many image formats, it only writes out one type of movie format - and that is AVI. Often AVI is all you'll want though (especially if you want a PowerPoint movie) and the instructions are as follows:
There are no options for AVI quality, but this is still very effective. See here for other methods to convert an image sequence to a movie.
Links
Retrieved from 'http://andrewnoske.com/w/index.php?title=ImageJ&oldid=417'
On this pageIntro to ImageJDownload and Install ImageJ
The ImageJ Toolbar Download Images Explore a Digital Image Investigate Pixel Data Play With Color Explore More If You Have Time
Movies on This Pagetop of page Intro to ImageJ
ImageJ is free public domain image processing software developed at the National Institutes of Health. Its power and flexibility allow it to be used as a research tool by scientists in many disciplines, from medicine to astronomy. Installers are available for Windows, MacOS and OSX, and Linux.
You can use ImageJ to display, annotate, edit, calibrate, measure, analyze, process, print, and save raster (row and column) image data. It reads most common raster image formats as well as raw data files in text format, such as from spreadsheets. ImageJ also supports stacks - multiple images in a single window - for animation and analysis.
Click on the movie to start playing.
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To help you become comfortable using geospatial technology, we have created a number of short videos that demonstrate basic operations and analysis techniques. These videos are embedded within the instructions throughout the pages of this course. You can quickly find them by looking for the movie camera icon. In addition, all the videos on a given page can be downloaded to your hard drive. You may find it useful to run these videos from your hard drive rather than the Internet, especially if your Internet connection is slow or unstable. The videos are available in flash video and iPod (mp4) formats. You may also use these videos in your teaching if you like. Download and access all the movies on a page from the Movies on this Page section at the bottom of the page.
top of page Download and Install ImageJ
Go to the ImageJ Download page , and download and install the application for your operating system.
Click the ImageJ Download page and it will open in a new window. Click the link that appears directly below the name of your computer's operating system (e.g. Mac, Linux, Windows). This action will transfer a compressed file of the software to your computer. Your browser should automatically expand the file, creating an ImageJ folder on your computer's hard drive.
For more details, or if you have problems running the application, access ImageJ's Installation Instructions then select your operating system.
Note to Windows Users: It is recommended that you install ImageJ in the Documents directory, rather than in the Program Files directory. For security reasons, Windows 7 and Windows Vista do not allow programs to alter themselves by writing files to the Program Files directory. If ImageJ is installed in the Program Files directory, then the update function in Step 2 below will not work properly.
top of pageUpdate ImageJ Software
Double-click the ImageJ icon to launch the application and choose Help > Update ImageJ... A window will appear, telling you the version you are currently running and a list of upgrade versions. Choose the version you want to upgrade to (usually the most recent, or default version) and click OK. After the update downloads, re-launch ImageJ to run the new version.
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Help with Updating ImageJ: Some users have reported problems updating ImageJ in certain versions of Windows. This is causing some of the tools and instructions (for example, setting the Threshold level for the Wand tool) to not function properly.
The quickest way to fix this is to reinstall ImageJ to the Documents directory. Alternately, you can manually update ImageJ with the instructions below:
The ImageJ Toolbar
The ImageJ toolbar contains both built-in and customized tools for manipulating images. Most of the tools are similar to those used in other graphics programs. You will learn about the tools as you use them.
top of page Download ImagesDownload two images of Lake Mead to your Week 2 folder or directory.
top of page Explore a Digital Image
In ImageJ, choose File > Open.., navigate to your Week 2 folder, and open the lake_mead_2004_grayscale.jpg file. This is a grayscale satellite image of the area around Lake Mead, Nevada, taken by one of the Landsat satellites.
Zoom in and out
The squares you see are the dots or pixels (short for picture elements) that make up the image. An important concept is that -- despite the impression given by those amazing FBI image processing techs you see in movies and television -- you can't zoom in to an image indefinitely. When you reach the point where you can distinguish the individual pixels, you won't see additional details by zooming in more.
top of page Scroll to move around
When you're zoomed in, how do you move around an image?
top of page Investigate Pixel DataBy the numbers - pixel values and coordinates
A digital image-- no matter where it comes from or how it is produced --is really just a string of numbers. Most of the time when you're working with digital images, the software keeps the numbers hidden from you. What makes ImageJ so useful is that you always have access to the numbers. Understanding this will help you and your students unlock the power of ImageJ.
An important concept here is that storing all this information in an image file on your computer is much more efficient than it seems. The computer doesn't need to store x- and y-coordinates -- just the pixel values, in one long string, plus the width and height of the image. The coordinates are just information about the pixel under the cursor -- its column and row number -- that the software reports to the user.
To reconstruct the image correctly, the computer just needs to 'know' the number of columns and rows in the image. This kind of grid of rows and columns is also called a raster, which is why this type of digital image is also called a raster image and why ImageJ is called a raster image processor.
top of page Play With ColorLookup tables
So far, you know that a digital image is a string of numbers arranged in rows and columns. How does the computer know what each number should look like when it displays that pixel on your screen? It's pretty simple, really. In addition to a string of numbers, the computer has a 'secret decoder ring' called a Lookup Table that it uses in paint-by-number fashion. In a very simple image with only four possible values, the lookup table might look like 0 = black, 1 = blue, 2 = red, 3 = white. In an 8-bit image, the 256 possible values correspond to 256 colors. (Okay, we know what you're thinking, but black, white and all those grays ARE colors!) The lookup table can be stored in the file with the data, or you can control it using the software that's displaying the data.
The key thing to remember about lookup tables is that they change the appearance of the image, not the pixel values themselves. The colors may change, but the numbers don't.
Now we can put it all together into a simple definition of a digital image:
Nih Fiji Download
A digital image is a series of numbers, arranged in a grid of rows and columns, and displayed according to a lookup table.
This image is an 8-bit image. Each pixel is represented in the computer's memory by an 8-bit binary number, representing 256 possible values from 0 to 254. Another term for the number of binary bits used to describe the value of a pixel is bit depth. You can think of the bit depth as the 3rd dimension of an image (width and height are the other two).
top of page Color images
top of page Explore More If You Have TimeWhen values represent something other than brightness
Resources
top of page Movies on this PageHow to download movies
Flash video versions
Download these versions to play on your computer. You'll need an appropriate movie player to view the file, such as Flash Player, Real Player (Mac / Win), or Adobe Media Player.
Quick Tour of ImageJUpdating ImageJ Zooming Scrolling Pixel Coordinates and Values Imagej Download For Mactop of pageiPod versions
Download these version to play on your iPod or iPhone.
Quick Tour of ImageJUpdating ImageJ Zooming Scrolling Imagej Download Mac DownloadPixel Coordinates and Values top of page Imagej Download MacComments are closed.
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