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Tools
ImageJ can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine.

ImageJ toolbar and clickable table of contents.
Area Selection Tools
Use these tools to create area selections that will be operated on separately from the rest of the image.
The contents of an area selection can be copied to the internal clipboard, cleared (to white), filled with
the current drawing color, outlined (using Edit>Draw), filtered, or measured.
Use the backspace key as a shortcut for Edit>Clear. Use Image>Colors>Color Picker to set the
drawing color. Double click on any line tool to change the line width used by Edit>Draw.
Use the arrow keys to "nudge" a selection one pixel at a time in any direction.
Rectangle
When creating the selection, drag with the shift key down to constrain it to a square.
Use the small "handle" in the lower right corner to resize. Use the arrow keys with
the alt key held down to change the width or height one pixel at a time.
As a selection is created or resized, its location, width and height are displayed in the status bar.
Hold the alt key down when moving or resizing to force the location and size to be
displayed in pixels.
With ImageJ 1.42 and later, hold the control key down (command key on Macs) to
resize around the center. With ImageJ 1.43 and later, hold the alt down to constrain
resizing to the current aspect ratio.
Oval
Creates an elliptical selection. Holding the shift key down forces the selection to be circular.
Use the arrow keys with the alt key pressed to change the width or height. As the selection
is created or resized, its width and height are displayed in the status bar. Right click or double click
on this tool to switch to the selection brush tool.
As with rectangular selections, hold the control key down (command key on Macs) to
resize around the center and the alt key to constrain
resizing to the current aspect ratio.
Selection Brush
This tool allows you to adjust the shape of an area selection using a
circular "brush". To expand a selection, click inside it and drag along
the boundary. To shrink it, click outside and drag along the bounday.
(With ImageJ 1.38 and earlier,
you have to hold down the alt key to do this.) To always add to the
selection, hold the shift key down. To always subtract from it,
hold the alt key down.
Double click on the tool icon to adjust the brush diameter.
The selection brush tool shares a toolbar slot with the oval selection tool. To switch to it,
double click on the oval tool and check "Enable Selection Brush" in the dialog. Or right
click on the oval tool and select "Selection Brush" from the drop down menu.
Polygon
Creates irregularly shaped selections defined by a series of line segments.
To create the selection, click repeatedly with the mouse to create line segments.
When finished, click in the small box at the starting point (or double-click),
and ImageJ automatically draws the last segment.
The points that define a polygon selection can be moved or deleted, and new points can be added.
To delete a point, click on it with the alt key down. To add a point, click on an existing point with the
shift key down.
Freehand
The freehand tool lets you create irregularly shaped selections by dragging with the mouse.
Wand Tool
Creates a selection by tracing objects of uniform color or thresholded objects.
To trace an object, either click inside near the right edge, or outside to the left
of the object. To visualize what happens, imagine a turtle that starts moving to
the right from where you click looking for an edge. Once it finds the edge, it
follows it until it returns to the starting point. Note that the wand tool may
not reliably trace some objects, especially one pixel wide lines,
unless they are thresholded (highlighted in red)
using the Image>Adjust>Threshold tool.
Use the WandAutoMeasureTool
macro to outline and automatically measure objects.
Composite Selections
Hold the shift key down when creating an area selection and it will be added to the
existing selection. Hold down the alt key and it will be subracted from the existing selection.
To add a non-square rectangle or ellipse, release the shift key after you start adding the selection.
Line Selection Tools
Use these tools to create line selections. Use Analyze>Measure to calculate the length of a line selection.
Use Edit>Draw to permanently draw the line on the image. Change the drawing color by
clicking in the Image>Colors>Color Picker window. Double click on any line tool to
specify the line width. Use the arrow keys to "nudge" a line selection one pixel at a time.
The three line selection tools share the same toolbar slot. To switch to a different tool, right
click on the current line tool and select the desired tool from the drop down menu.
Straight Line
Use this tool to create a straight line selection.
Holding the shift key down forces the line to be horizontal or vertical.
When creating a line on a zoomed image, holding the alt key down forces the two points that
define the line to have integer coordinate values.
With ImageJ 1.42 and later, holding the control key down (command key down on Macs) while moving
either end of the line rotates/resizes it about its center. With ImageJ 1.43 and later, holding the
alt key down while moving either end of the line keeps the line length fixed.
To spatially calibrate an image, create a line selection corresponding to a known distance (e.g. 10mm),
then enter that distance in the Analyze>Set Scale dialog box.
Segmented Line
Create a segmented line selection by repeatedly clicking with the mouse.
Each click will define a new line segment. Double-click when finished, or click in the
small box at the starting point.
The points that define a segmented line selection can be moved or deleted, and new points can be added.
To delete a point, click on it with the alt key down. To add a point, click on an existing point with the
shift key down.
Freehand Line
Select this tool and drag with the mouse to create a freehand line selection.
Angle Tool
This tool allows you to measure an angle defined by three points. The angle is displayed in the status bar while the selection
is being created or adjusted. Press "m" (Analyze>Measure) to record the angle in the Results window.
Point Selection Tool
Use this tool to create a point selection, to count objects or to record coordinates.
Click once to create a single
point selection. Shift-click to add more points. Click on a point and drag to move it.
Alt-click on a point to delete it.
Alt-click and drag with the rectangular or oval selection tool to delete multiple points.
Double-click on the point tool icon to display the following configuration dialog box.
![[Point Tool Dialog]](/web/images/stories/imagej/point-tool-dialog.jpg)
If Auto-Measure is checked,
clicking on an object in the image records its location and intensity and, if Mark Width is greater than zero,
draws a mark in the current foreground color. The marks modify the image so it may be wise to work with a copy.
Set the mark width to zero to disable marking.
Note that color marks are only available with color images
or grayscale images that have been converted to RGB.
If Auto-Next Slice is checked, ImageJ will advance to the next stack slice after each measurement is recorded.
Use the Edit>Draw command to permanently draw a circular marker on the image at the
location of each point.
The makers are drawn in the current foreground color using a diameter of Mark Width.
Text Tool
Use this tool to add text to images. It creates a rectangular selection containing one or more lines of text.
Use the keyboard to add characters to the text and the backspace key to delete characters.
Use Edit>Draw to permanently draw the text on the image. Use Edit>Options>Fonts,
or double-click on the text tool, to specify the typeface, size and style.
Magnifying Glass
Click on the image with this tool to zoom in. Alt-click (or right-click) to zoom out.
The current magnification is shown in the image's title bar.
Double-click on the magnifying glass icon to revert to the image's original magnification.
There are 21 possible magnification levels:
3.1, 4.2, 6.3, 8.3, 12.5, 16.7, 25, 33.3, 50, 75,
100, 150, 200, 300, 400, 600, 800, 1200, 1600, 2400 and 3200 percent. When zooming in, press the
shift key to prevent the window from being enlarged.
Scrolling Tool
Allows you to scroll through an image that is larger than its window. When using other tools (except the text tool),
you can temporarily switch to this tool by holding down the space bar.
Color Picker
Sets the foreground drawing color by "picking up" colors from images.
The color of this tool's icon changes to match the drawing color.
Colors can "picked up" from the Image>Colors>Color Picker window using any tool.
Alt-click in the Color Picker to change the background color.
Double-click on this tool to display the Color Picker.
The icon for this tool is drawn in the current foreground color and
the frame around it is drawn in the current background color.
Macro Tools
The tools on the right side of the toolbar are defined by macros in the StartupMacros file, which can be opened using the
Plugins>Macros>Startup Macros command. These tools can be customized by editing the StartupMacros file,
or replaced entirely using the
menu at the right end of the toolbar.
The macro language documentation has
more information
about macro tools.
Abort Tool This
macro tool aborts the currently running macro or plugin. It is
equivalent to pressing the esc key. It is defined in the StartupMacros
file
by this macro:
macro "Abort Action Tool - CbooP51b1f5fbbf5f1b15510T5c10X" {
setKeyDown("Esc");
}
Menu Tools These
three menus are are created by macros in the StartupMacros file. They
provide convenient access to commands that are also
in the main ImageJ menu bar, but buried two or three levels deep. The
"Dev" (Developer) menu contains commands frequently used by ImageJ
macro and plugin developers. The "Stk" (Stack) menu duplicates the
commands in the Image>Stacks submenu. The "Lut" menu
lists all the LUTs (Lookup Tables) in the ImageJ/luts folder.
Drawing Tools
The drawing tools are defined by macros in the StartupMacros file. The
tools draw (or fill) in the current foreground color, or in the background
color if the alt key is down. Set the foreground and background
colors by double-clicking on the on the eye dropper (color picker) tool.
Double-click on the pencil, paintbrush or arrow
tool to set the drawing width for that tool. Double-click
on the flood fill tool to select the fill method, either 4-connected or 8-connected.
Macro Toolset Switcher
Use this drop down menu to switch to alternative macro tool sets located in the ImageJ/macros/toolsets folder, or
to revert to the default ImageJ/macros/StartupMacros tool set.
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