ImageJ is an open-source image processing program originally created in 1987 as NIH Image. It was later rewritten in Java as ImageJ in 1997. Key features include support for a wide range of image formats, macro scripting, plugins, and its use in scientific image analysis. ImageJ is widely used for tasks like particle analysis, image segmentation, image enhancement, and more. It has a large user community and active development of new plugins and extensions.

1. : ImageJ

2. ImageJ (ImageJ ≠ Photo Shop)
•
• 1987 : NIH Image
• 1997 : ImageJ (Image Processing and Analysis in Java)
• 2007 : FIJI
• 2009 : ImageJ2
• Pascal
• Mac
•
• Java
• Windows Mac Linux
•
• ImageJ ( ImageJ2 )
• 3
• (JavaScript Jython ImageJ Macro…)
• ImageJ
•
•

3. ImageJ
• ImageJ HP (https://imagej.nih.gov/ij/)

4. Java
• Java HP (https://www.java.com/)

5. FIJI ImageJ2
• FIJI
• https://fiji.sc/
• ImageJ2
• https://imagej.net/

6. ImageJ
← Menu Bar
← Tool Bar
← Status Bar
Windows (7)
MacOS (High Sierra)
← Menu Bar
← Tool Bar
← Status Bar
Windows MacOS

7. ImageJ
FIJI
ImageJ2 ⇒ Plugins -> Utility -> Find Commands

8. ImageJ FIJI
<ImageJ>
-> Image -> Process -> Analyze
<ImageJ> <ImageJ><FIJI> <FIJI> <FIJI>

9. ImageJ
• ImageJ DICOM
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•
• PowerPoint
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•
•
•

10. •
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•

11. ( ) - Image
• ImageJ
• File -> Open ->
•
•
•
Open Samples > Lena (68K)

12. ImageJ
• (8-bit and 16-bit)
• (32-bit)
• (24-bit RGB and 32-bit RGBA)
⇒ TIFF DICOM AVI
• DICOM
• Tag Rescale Intercept Slope
⇒ CT CT PET Bq/cc
•
•
•
• gray = (red + green + blue)/3
• gray* = 0.299 red + 0.587 green + 0.114 blue
*: Edit -> Options -> Conversions “Weighted RGB to Grayscale Conversion”
• MATLAB (rgb2gray): 0.2989 red + 0.5870 green + 0.1140 blue

13. • Image -> Lookup Tables
•
• ⇒ Lookup Tables
• Image -> Color -> Display LUTs

14. ( ) - Stacks
• ImageJ
• File -> Import -> Image Sequence ->
• Image -> Stacks -> Images to Stack
•
•
• Multi Frame DICOM
File -> Open
Open Samples > T1 Head (2.4M, 16-bit)

15. • Image -> Stacks -> Make Montage
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•

16. • Image -> Stacks ->Reslice & Make Montage
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• Output spacing (mm) Tag
Pixel Size

17. • Image -> Stacks -> Orthogonal Views
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•
•
•

18. • Image -> Stacks -> 3D Projection
DICOM Header

19. •
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20. • Analyze
• Measure ( )
• Analyze Particles ( )
• Summarize ( )
• Distribution ( )
• Label ( )
• Clear Results Set Measurements ( )
• Set Scale ( )
• Calibrate ( )
• Histogram ( )
• Surface Plot ( )
• Gels ( )
• Tools ( )
• Analyze Line Graph ( )
• ROI Manager (ROI )
• Calibration Bar ( )

21. Catphan®600
• Catphan®
• (Region of Interest: ROI)
•
120 kV, 350 mA 120 kV, 100 mA

22. Catphan®600
• Uniformity Module
• 5
•
Catphan®600

23. -
• Tool Bar area selection tools
(Region of Interest: ROI)
<area selection tools>
<line selection tool>
<angle tool>
( )
ROI
(x, y)
(w, h)

24. -
• Analyze -> Tools -> ROI Manager
• More -> Specify
• ROI
•
•
• ( )

25. -
(x, y) (x, y)
Height Height
Width
• (0, 0) ← (1, 1)
• Oval:
• Constrain square/circle:
• Center:
Width

26. • Analyze -> Tools -> ROI Manager
• Add
• [Add]
•
• More -> Save
• ROI Manager
ROI
• ROI .roi
• ROI .zip
• More -> Open
• ROI

27. Area ( )
Mean Gray Value
Standard Deviation
Modal Gray Value
Min & Max Gray Value &
Centroid
Center of Mass ( )
Perimeter
Bounding Rectangle
Fit Ellipse
Shape Descriptors (Circularity: 4π / 2 (1 = ))
Integrated Density
[IntDen: ][RawIntDen: ]
Median
Skewness 3 ( : )
Kurtosis 4 ( : )
Area Fraction ( 0 )
Stack Position ( ) (Ch Slice Frame)
Analyze -> Set Measurements
Analyze -> Measure

28. • Analyze -> Tools -> ROI Manager -> Measure
• Analyze -> Measure
• ROI
120 kV, 350 mA
• Mean: 13.695 - 14.708
• StdDev: 12.389 - 14.866
120 kV, 100 mA
• Mean: 12.967 - 14.215
• StdDev: 20.827 - 24.349

29. •
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•
•

30. • Process
• Smooth ( )
• Sharpen ( )
• Find Edges ( )
• Find Maxima… ( )
• Enhance Contrast… ( )
• Noise ( )
• Shadows ( )
• Binary ( )
• Math ( )
• FFT ( )
• Filters ( )
• Image Calculator… ( )
• Subtract Background… ( )
• Repeat Command ( )

31. Filters: / /
• Process
• Process -> Filter
Original Smooth Sharpen Find Edges
Gaussian Unsharp Mask Variance

32. Filters:
• Process -> Filters -> Convolve
•
•
• Excel
-2 -1 0
-1 1 1
0 1 2
0 1 0
1 -4 1
0 1 0

33. • Catphan Phantom
120 kV, 350 mA
• Mean: 13.695 - 14.708
• StdDev: 12.389 - 14.866
120 kV, 100 mA
• Mean: 12.967 - 14.215
• StdDev: 20.827 - 24.349
120 kV, 100 mA
with Gaussian Filter σ = 0.7
• Mean: 12.975 - 14.232
• StdDev: 13.993 - 16.959

34. • Analyze -> Histogram
•
Standard Image Data-BAse (SIDBA) Barbara (Monochrome Image)

35. •
•
( )
•
• Process -> Enhance Contrast
• CNN
•
Original Enhance Contrast

37. •
•

38. • Image -> Color -> Split Channels
• red green blue
• Image -> Color -> Merge Channels
•
< > < >
(red)
(green)
(blue)

39. • File -> Save As
•
• DICOM
• Plugin
• Tiff
• 16-bit
•
• ⇒
• (Text Image)
•
• Excel
•
• AVI Animated GIF ⇒ PowerPoint

40. PowerPoint
• PowerPoint ( )
• ImageJ
ImageJ
: 100%
PowerPoint
: 6405%

41. •
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42. • Plugin Macro ImageJ
• Plugin Java
• ImageJ Java Compiler .class Compile
• Macro Java ImageJ
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• Plugin Macro
• Plugin:
• Macro:
•
• https://imagej.nih.gov/ij/plugins/

43. • ImageJ1 FIJI (Windows) ImageJ2 (Windows )
• Plugins Macros ImageJ/plugins
• “_”
• FIJI (Mac) ImageJ2 (Mac)
•
Fiji.app(ImageJ.app)/plugins

44. ImageJ Hello, World!
• Plugin -> New -> Plugin
• File -> Compile and Run
• “_”
• Plugin
• Plugin -> Macros -> Edit
•
Plugin

45. ImageJ (FIJI) Python!
• Jython: Java Python
• CPython
• Python
• Java
• CPython
• ImageJ Python
ImageJ/plugins/jars/Jython.jar
• .py

46. Plug-in - DICOM Wright -
• ImageJ
DICOM
• Plug-in (The Tudor DICOM Tools)
• http://santec.tudor.lu/project/dicom
•
• DICOM
• DICOM
• Multi Flame

47. Plug-in - PET/CT Viewer -
• PET/CT Viewer
• (Nuclear Medicine at Beth Israel
Deaconess Medical Center, Boston MA.)
• FIJI
• Updater

48. Plug-in - PET/CT Viewer -
• FIJI PET/CT Viewer
• OsiriX
Fusion Viewer
• SUV Tag SUL
PET CT Fusion MIP
Axial
Coronal

49. • ImageJ
• ImageJ
•
ImageJ