J Image Fiji Download For Mac

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Fiji is a distribution of ImageJ which includes many useful plugins contributed by the community.

Click on Help Update. After Updater scans for updates, click the 'Manage update sites' button. Click 'Add update site'. In the new line, add the following. Click the checkbox to enable updates. Click 'Apply changes'. After the update completes, restart Fiji. The “Protein Array Analyzer” gives a friendly way to exploit this type of analysis, thus allowing quantification, image modeling and comparative analysis of patterns. The Protein Array Analyzer, which was programmed in ImageJ’s macro language, is an extention of the Dot Blot Analyzer2 3 a graphically interfaced tool that.

  • In the general case, under Mac OS X or Linux, you can copy or move the files to a directory listed in your PATH, e.g. Under Mac OS X, this will be done automatically if you install from the.pkg file. Using the software. To use the ImageJ NDPITools plugins, you can read the specific instructions. The rest of this page deals.
  • Tested with Fiji/ImageJ v1.47/v1.48; 3D-imagetime-interpolator.ijm is a macro that generates intermediate 3D images between two initial 3D images. Interpolation is linear for each pixel. This was created for visual creation purpose only. To use it, open your two 3D images in ImageJ and run the macro.
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Fiji is supported on the following systems:

  • Windows XP, Vista, 7, 8 and 10
  • Mac OS X 10.8 “Mountain Lion” or later
  • Linux on amd64 and x86 architectures

However, Fiji (like ImageJ) should run on any system for which a Java 8 runtime is available (Solaris, Raspbian, etc.).

Caution: “Program Files” not recommended!

If you are installing ImageJ on Windows, we strongly recommend that you storeyour ImageJ.app directory somewhere in your user space(e.g., C:Users[your name]ImageJ.app) rather than in C:Program Files orother system-wide directory. If you move ImageJ.app to such a directory, modernversions of Windows will deny ImageJ write permission to its own directorystructure, preventing it from being able to update. See alsoimagej/imagej#72.

Packages for Debian / Ubuntu

We used to offer Debian packages of Fiji. Unfortunately, for several reasons,we are withdrawing support for these packages until such time as someone isable to maintain them properly, so please switch to using the Linux downloadsabove instead.

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If you are a Debian packaging expert who would like to address this situation,we would love to have your help—please join us in chat or on theforum.

Fiji is distributed as aportable application.That means that you do not have to run an installer; just download, unpack andstart it.

  • Many common questions are answered on the FAQ.
  • If you encounter bugs, please see the Getting Help page.

See the source code page for details on obtaining the Fiji source code.


You can download previous Fiji builds by date stamp from the archive.

Life-Line Fiji versions

This sections offers older downloads of Fiji, preserved just prior to introducing major changes. The idea is that if something goes horribly wrong, you can fall back to a stable version.

Java 8

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Here are Life-Line versions of Fiji created after the switch to Java 8.

2017 May 30Just prior to a sweeping update to nearly all components.

Java 6

Here are Life-Line versions from before Fiji switched to Java 8.

2017 May 30 The final version of Fiji using Java 6, for all platforms.
2015 December 22 Just prior to starting the transition to Java 8.
2014 November 25 Just prior to a big update to facilitate reproducible builds.
2014 June 02 Just prior to some big changes to ImageJ2 under the hood.
2013 July 15 Just prior to extensive changes reconciling Fiji with ImageJ2.

See also

  • https://downloads.imagej.net/fiji/ for early versions of Fiji, and other miscellany.

On this page

Getting to Know Measuring in ImageJ

Select What You Want to Measure (Set Measurements)
Finding the Image Scale
Set a Scale Using an Existing Scale Bar
Set a Scale Using a Known Distance
Set a Scale Using the Image Resolution
Add a Scale Bar
Explore Image Scale and Measurement
Movies on This Page

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Getting to Know Measuring in ImageJ

In the Intro toImageJ section, you learned that a digital image is a string of numbers, displayed in a rectangular array, according to a lookup table. You also learned about the three dimensions of an image width, height, and bit depth. The power of image processing is its ability to make measurements in these dimensions:

Spatial measurements Measurements of distance, area, and volume. These involve the first two dimensions of the image, its width and height.

Density measurements Measurements involving the third dimension, the pixel values. Pixel values can represent temperature, elevation, salinity, population density, or virtually any phenomenon you can quantify.

Before you can make meaningful measurements, you need to calibrate the image that is, 'tell' the software what a pixel represents in real-world terms of size or distance (spatial calibration), in terms of what the pixel values mean (density calibration), or both. In this section, you will learn how to spatially calibrate digital images.

  • Launch ImageJ by double-clicking its icon on your desktop or by clicking its icon in the dock (Mac) or Launch Bar (Win).
  • Choose File > Open..., navigate to your Week 2 folder or directory, and open the lake_mead_2004_color.jpg image that you downloaded in the Intro to ImageJ section.

This image is a Landsat view of Lake Mead, Nevada, taken in May 2004.

Spatially calibrating an image is commonly called setting the scale, and an image that has a scale set so that distances and areas are in units other than pixels is called a spatially calibrated image.
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Select What You Want to Measure

ImageJ can collect a number of measurements for you. Before you begin setting a scale and making measurements you need to decide on your measurement options.

  1. Choose Analyze > Set Measurements....
  2. The Set Measurements window opens. Check Area and Perimeter (length) to collect those measurements. Then click OK.

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Find the Image Scale

If you measure distances or areas on a digital image, your results will be expressed in pixels and square pixels. ('Wait,' you say, 'Aren't all pixels square?' Actually, no. But that's a topic for another time...) If you want to measure image features in units like meters or square miles, you need to convert pixels to their equivalent 'real world' units. You could do this yourself with a calculator, or you could have ImageJ do the work for you. ('Yesssssss!') Giving ImageJ the information it needs to convert from pixels to other units is called setting the scale.

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To set the scale in ImageJ, you need to know what the scale is. Here are some ways you can find the scale of an image:

  • A scale bar is printed on the image.
  • There is a known distance in the image, such as the distance between two landmarks.
  • A written statement of scale exists, usually in the image documentation. In this case, the scale may also be called the image resolution. For example, if the image documentation says the resolution is 30 meters, then the scale is '1 pixel = 30 meters.'
  • Copy the scale from another image of the same scale that has a scale bar or known distance in it.

Set a Scale Using an Existing Scale Bar

Someone was kind enough to put a scale bar on this Lake Mead image, so we'll use it to set the scale.

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  1. Use the straight line selection tool to drag out a line across the scale bar. Select Analyze > Set Scale... The Set Scale window opens. The distance you measured in pixels will be displayed. Enter 45 for the Known Distance and km or kilometers for the Unit of Length. To redo your line, click on the arrow tool, then re-click on the line selection tool. This effectively resets the tool.

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  • Using the straight line selection tool , click on one end of the scale bar, drag to the other end of the scale bar, and click again. (Tip: If you hold down the shift key while selecting with this tool, it forces your selection to be perfectly horizontal.)
  • Choose Analyze > Set Scale....
  • The Set Scale window opens. The distance you measured in pixels will be displayed. In this case, we got 261 pixels. Your mileage, er pixelage will vary, but it should be close to this. Enter 45 for the Known Distance and km or kilometers for the Unit of Length. For reference, the scale (in this case, 5.8 pixels per kilometer) is displayed at the bottom of the window. Then click OK.