home | contents | previous | next
The ImageJ plug in assists in manually tracking chemotactical or migration data. Recommended by ibidi for tracking cells; Allows quantification of cell movement between frames of a temporal stack. Version 1.6 1 Getting Started 1.1 About ImageJ1 ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any. Wayne, On OS X, you can go one step better. Double click on one of the.lut files. Of course the operating system will ask what application should it use to open these types of files. Once you specify ImageJ, then you can put the folder full of LUTS into the dock. If you click and hold on the folder in the dock, you get what amounts to a menu of LUTS from which you can chose the LUT you wish. Go to the download page: Select appropriate software, fill out form, follow instructions. (The Mac application is the same as that available from NIH above, with additional commands for accessing the Scion imaging boards. A few images are available at this site. Most images, and macros are available at the NIH.
Type Submenu
Use this submenu to determine the type of the active image or to convert it to another type.8-bit
Converts to 8-bit grayscale. The active image must be 16-bit grayscale, 32-bit grayscale, 8-bit color or RGB color.ImageJ converts 16-bit and 32-bit images and stacks to 8-bits by linearly scaling from min-max to 0-255, where min and max are the two values displayed in the Image>Adjust>Brightness>Contrast tool. Image>Show Info displays these two values as the 'Display range'. Note that this scaling is not done if 'Scale When Converting' is not checked in Edit>Options>Conversions.
RGB images are converted to grayscale using the formula gray=(red+green+blue)/3 orgray=0.299red+0.587green+0.114blue if 'Weighted RGB to Grayscale Conversion' is checked in Edit>Options>Conversions.
16-bit
Converts to unsigned 16-bit grayscale. Theactive image must be 8-bit grayscale or 32-bit grayscale.32-bit
Converts to signed 32-bit floating-pointgrayscale. The active image must be 8-bit grayscale or 16-bit grayscale.8-bit Color
Converts to 8-bit indexed color usingHeckbert's median-cut color quantization algorithm. A dialog box allows the number of colors (2-256) to be specified.The active image must be RGB color.RGB Color
Converts to 32-bit RGB color. The activeimage must be grayscale, 8-bit Color, or an RGB (red, green, blue) or HSB (hue, saturation and brightness) stack.RGB Stack
Converts to a 3-slice (red, green, blue)stack. The active image must be RGB color.HSB Stack
Converts to a 3-slice (hue, saturation andbrightness) stack. The active image must be RGB color.An attempt to perform an unsupported conversion causes a dialog box to be displayed that lists the possible conversions.The * indicates that both single images and stacks can be converted.Adjust Submenu
This submenu contains commands thatadjust brightness/contrast, threshold levels and image size.Brightness/Contrast...
Use this tool to interactively alter the brightness and contrast of the active image. With 8-bit images, brightness and contrast are changed by updating the image's look-up table (LUT),so pixel values are unchanged. With 16-bit and 32-bit images, the display isupdated by changing the mapping from pixel values to 8-bit display values, so pixel pixel values are also unchanged.Brightness and contrast of RGB images are changed by modifying the pixel values.Press shift-c to open the B&C window the quick and easy way. If it is already open, it is activated.
The line graph at the top of the window, which us superimposed on the image's histogram, shows how pixel values are mapped to 8-bit (0-255) display values.The two numbers under the plot are the minimum and maximum displayed pixel values. These two values define the display range, or 'window'. ImageJ displays images bylinearly mapping pixel values in the display range to display values in the range 0-255.Pixels with a value less than the minimum are displayed asblack and those with a value greater than the maximum are displayed as white.
There are four sliders. Minimum and Maximum control the lower and upper limits ofthe display range.Brightness increases or decreases image brightness by moving thedisplay range. Contrast increases or decreases contrast by varying the width of the display range.The narrower the display range, the higher the contrast.
Click on Auto, and ImageJ willautomatically optimize brightness and contrast based on an analysis of the image's histogram. Create a selection, andthe entire image will be optimized based on an analysis of the selection. The optimization is done by allowing a smallpercentage of pixels in the the image to become saturated (displayed as black or white). Each additionalclick on Auto increases the number of saturated pixels and thus the amount of optimization.
Click on Reset to restore the originalbrightness and contrast settings. The display range is set to the full pixel value range of the image.A resetMinAndMax() macro call is generated if the command recorder is running.
Click on Set to enter the minimum and maximum display range values in a dialog box. A setMinAndMax() macro call is generated if the command recorder is running.
Click on Apply toapply the current display range mapping function to the pixel data.If there is a selection, only pixels within the selection are modified. This option currently only works with 8-bit images and stacksand with RGB stacks. This is the only B&C option that alters the pixel data of non-RGB images.
With DICOM images, ImageJ sets the initial display range based on the Window Center (0028,1050) and Window Width (0028,1051) tags. Click Reset and it sets the display range to the minimum and maximum pixel values. As an example, the File>Open Samples>CT image has a Window Center of 50 and Window Width of 500, so the display range is set to -200 to 300(center-width/2 to center+width/2). Click Reset and the display range is set to -719 to 1402. Press 'h' (Analyze>Histogram) and you will see that the minimum pixel value in the image is -719 and the maximum is 1402. To display the DICOM tags, press 'i' (Image>Show Info). Press 'r' (File>Revert) to revert to the initial display range.
Threshold...
Use this tool to automatically or interactively set lower and upper threshold values, segmenting the image into features of interest andbackground. The thresholded features are displayed in red and background is displayed in grayscale.Use Analyze>Measure (with 'Limit to Threshold' in Analyze>Set Measurements
Use the upper slider to adjust the minimum threshold value and the lower one to adjust the maximum.Hold the alt key down while adjusting the minimum to move a fixed-width thresholding window across the range of gray values. Check Dark Background if the features are lighter than the background.
Thanks to Gabriel Landini, the drop down menu on the left allows any of 16 different automatic thresholdingmethods to be selected. These methods are described on Gabriel's Auto Threshold pluginwebsite. The 'Default' method isthe modified IsoData method used by ImageJ 1.41 and earlier.
Use the drop down menu on the right to select one of three display modes. Red displays the thresholdedvalues in red. B&W switches to a mode where features are displayed in black and background in white.Over/Under displays pixels below the lower threshold value in blue, thresholded pixels in grayscale,and pixels above the upper threshold value in green.
The Auto button uses the currentlyselected thresholding method to automaticallyset the threshold levels based on an analysis of the histogram of the currentimage or selection. Apply sets thresholded pixels to black and all other pixels to white. Reset disablesthresholding and update the histogram. Click on Set to enter new threshold levels into a dialog box.
Size...
Scales the active image or selection to aspecified width and height in pixels.Check Constrain Aspect Ratio to create an image with the specified width and have ImageJ adjust the height tomaintain the original aspect ratio. Check Interpolate to use bilinear interpolation. Set New width to 0to create an image with the specified height and have ImageJ adjust the width to maintain the original aspect ratio.
Canvas Size...
Changes the canvas size of an image or stack without scaling the actual image. The width and height may be either expanded or contracted. If the canvas size is increased, then the border is filled with the current background color. Or, if Zero Fill is checked, the border is filled with pixels that have a value of zero. Use the Image>Color>Color Picker tool to change the background color. The position of the old image within the new canvas may also be specified.Show Info...
Opens a text window containinginformation about the active image. For DICOM and FITS images, also displays file header information. Use the popup menu(right-click in the Info window) to save the information to a text file or copy it to the system clipboard.Properties...
Use this command to display and set various properties of the current image or stack.The number of Channels, Slices and Frames (c, z, and t) in the image can be changed as long as the product of c, z, and tis equal to the number of images in the stack.
The Unit of Length (a string describing the measuring unit), Pixel Width, Pixel Height and Voxel Depth(all in the Unit of Length unit) can be set. The width, height and depth are automatically convertedif Unit of Length is changed from one known unit ('nm', 'um', 'micron', 'mm', 'cm', 'meter', 'km' or 'inch') to another.
With t-series stacks, the Frame Interval in seconds (reciprocal of the frame rate) can be viewed and set.Origin (always in pixels) is the reference point (0,0) of the image coordinate system.Check Global to make the current settings global (i.e., apply to all images opened during the current session).
Color Submenu
This submenu contains commands that deal with color images.Split Channels
Splits an RGB image into sepate channels (images).Also splits RGB stacks into three separate stacks.The image names have ' (red)', ' (green)' and ' (blue)' appended to them. With composite images and/or hyperstacks (e.g., the 'Organ of Corti' sample image),this command splits the stack into sepate channels.Merge Channels...
Merges 1-4 greyscale images or stacks into an RGB image or stack.Select *None* to keep a channel empty (filled with 0).Check 'Create Composite' to convert 2-4 grayscale images or stacks into a composite image or hyperstack.Check 'Keep Source Images' if you wish to keep the originals.Arrange Channels...
This command allows you to change the order of the channels in a hyperstackby entering the channel numbers in a different order.Channels that do not appear in the bottom row of thumbnail images will be deleted. Click on any thumbnail image to change that channel's color LUT.When calling this command from script or macro, you also can duplicate channels, e.g.:
Channels Tool...
Opens the 'Channels' window, or brings it to the front if it is already open.Shift-z is the keyboard shortcut for this command.Stack to RGB
Converts a two or three slice stack into an RGB image,assuming that the slices are in R, G, B order.The stack must be 8-bit or 16-bit grayscale.Also converts composite images (e.g., the HeLa Cells sample image) into RGB.Make Composite
Converts an RGB image, a 2-7 image stack or a 2-7 channel hyperstackinto a composite color image. Use the 'Channels' tool (press shift-z top open) toenable and disable the channels of a composite image. Use the 'B&C' tool(press shift-c to open) to adjust the brightness and contrast of the current channel.In the example above, all but the red and blue channels of a five channel composite image havebeen disabled using the 'Channels' tool and the 'B&C' tool is being usedto adjust the brightness and contrast of the blue channel.
Show LUT
Displays a plot of the active image's lookup table. The lookup table, or color table, describes the color that is displayed for each of the 256 possible pixel values. For 16 and32 bit images, the range of displayed pixel values is mapped to 0-255. A bar under the plot displays the color representation of the pixel values. Note that RGB color images do not use a lookup table.Edit LUT
Opens the ImageJ LUT (Lookup Table) Editor. A lookup table (LUT) in ImageJhas up to 256 entries. The entry index, and the three values (red, green and blue) associated with it,are displayed in the ImageJ status bar as you move the cursor over the LUT Editor window.Click on an entry to edit the red, green and blue values for that entry.Drag across several entries and you will be asked to define the RGB starting and ending values for theselected range. The Editor will fill the remaining entries using the selected interpolation method(Replication, Interpolation or Spline Fitting).
You can define the number of entries in the LUT usingthe 'Set' option. When increasing the number of entries, the Editor uses the specified interpolationmethod. Replication just repeats the entrieswhile Interpolation and Spline Fitting produce gradations between the colors.The 'Invert' button sets the inverse of the LUT RGB entries. 'Open' and 'Save' allow importing or exporting the LUTs.
Color Picker...
The Color Picker tool enables theuser to select foreground and background colors, which affect Edit>Fill, Edit>Draw and other color drawing commands. It displays current foreground and background colors inthe selection boxes at the bottom of the window. It has two modes:foreground and background. To change modes, click on the desiredselection box. Clicking on the Foreground/Background Switcher button sets the current foreground to the background and vice versa. The Black/White Reset button sets the foreground to black and the background to white.The color palette is based on HSB (Hue, Saturation and Brightness) color model. Hue increases as you go down the palette while saturationand brightness values are split horizontally. The left half of the palette varies onlyin brightness while the right half varies only in saturation. At thecenter of the color ramp are enlarged red, green, blue, cyan, magenta,and yellow colors for quick selection. To the left of the color palette is a grayscale ramp that goes from pure black to pure white.
Double-clicking on a color brings up the Color Selector, shown on the right inthe illustration. Use the sliders to specify the RGB values ofthe foreground or background color. To get precise colors, manually change the values in the text boxes. The title of the Color Selector window ('Foreground Color' or 'Background Color') indicates the current selection mode.
The Color Picker was written by Gali Baler, a 2003-2004 intern from Bethesda-Chevy Chase High School.
Stacks Submenu
This submenu contains commands that workwith stacks.Add Slice
Inserts a blankslice after the currently displayed slice. Hold down the alt key to add the slice before the current slice.Delete Slice
Deletes the currently displayed slice.Next Slice
Displays the slice that follows thecurrently displayed slice. As a shortcut, press the '>' key.Previous Slice
Displays the slice that precedes thecurrently displayed slice. As a shortcut, press the 'Set Slice...Displays a specified slice. The user must entera slice number greater than or equal to one and less than or equal to the number of slices in the stack.Convert Images to Stack
Creates a new stackconsisting of all images currently displayed in separate windows. Theimages must all be the same type and size.Convert Stack to Images
Converts the slices in thecurrent stack to separate image windows.Make Montage
Produces a single image which containsthe images from a stack displayed in a grid format. This can be useful for visual comparisons of a series of imagesstored in a stack. A dialog box allows you to specify the magnification level at which the images are copied, and toselect the layout of the resulting grid.With ImageJ 1.35m or later, check Use Foreground Color to draw bordersand labels in the foreground color and to fill blank areas with the background color.Use theMontage Shuffler tool macroto reorder the images in the montage.Reslice...
Reconstructs one or more orthogonal slices through the image volume represented by the current stack. A dialog allows you tospecify the spacing of the reconstructed slices.Output spacing determines the number of orthogonal slices that will reconstructed.Increasing Output spacing reduces the size of the output stack.With straight line selection, the number of orthogonal slicesgenerated is determined by the value of the 'Slice count'�field.Output spacing is ignored with line selections and one orthogonalslice is generated for each time point.
The Start at menu has four choices:
- Top - Start reconstructing slices at the top of the image
- Left - Start reconstructing at the left edge of the image
- Bottom - Start reconstructing at bottom of the image
- Right - Start reconstructing at the right edge of the image
Check Flip vertically and each slice in the output stack will be flipped vertically.Check Rotate 90 degrees and each slice in the output stack will be rotated 90 degrees.Check Avoid interpolation and no interpolation will be done.
The estimated size of the output stack and the amount of available memory are displayed at the bottom of the dialog.Increase Output Spacing to reduce the size of the output stack.
This plugin, and the ZProject plugin, were contributed by Patrick Kelly and Harvey Karten of theUniversity of California, San Diego.
ZProject...
Projects an image stack along the axis perpendicular to image plane (the so-called 'z' axis). Four different projectiontypes are supported. Average Intensity projection outputs an image wherein each pixel stores average intensityover all images in stack at corresponding pixel location. Maximum Intensity projection creates an output imageeach of whose pixels contains the maximum value over all images in the stack at the particular pixel location. SumSlices creates a real image that is is sum of the slices in the stack. Standard Deviation creates a realimage containing the standard deviation of the slices.3D Project...
Generates an animation sequence by projecting through a rotating 3D data set onto a plane. Each frame in the animationsequence is the result of projecting from a different viewing angle. To visualize this, imagine a field of parallel rayspassing through a volume containing one or more solid objects and striking a screen oriented normal to the directions ofthe rays. Each ray projects a value onto the screen, or projection plane, based on the values of points along its path.Three methods are available for calculating the projections onto this plane: nearest-point, brightest-point, andmean-value. The choice of projection method and the settings of various visualization parameters determine how bothsurface and interior structures will appear.This routine was written by Michael Castle and Janice Keller of the University of Michigan Mental Health ResearchInstitute (MHRI).
Select Nearest Point projection to produce an image of the surfaces visible from the current viewing angle. Ateach point in the projection plane, a ray passes normal to the plane through the volume. The value of the nearest nontransparent point which the ray encounters is stored in the projection image. Brightest Point projection examinespoints along the rays, projecting the brightest point encountered along each ray. This will display the brightestobjects, such as bone in a CT (computed tomographic) study. Mean Value projection, a modification ofbrightest-point projection, sums the values of all transparent points along each ray and projects their mean value. Itproduces images with softer edges and lower contrast, but can be useful when attempting to visualize objects containedwithin a structure of greater brightness (e.g. a skull).
Slice Interval is the interval, in pixels, between the slices that make up the volume. ImageJ projects the volumeonto the viewing plane at each Rotation Angle Increment, beginning with the volume rotated by InitialAngle and ending once the volume has been rotated by Total Rotation.
The Lower and Upper Transparency Bound parameters determine the transparency of structures in the volume.Projection calculations disregard points having values less than the lower threshold or greater than the upperthreshold. Setting these thresholds permits making background points (those not belonging to any structure) invisible.By setting appropriate thresholds, you can strip away layers having reasonably uniform and unique intensity values andhighlight (or make invisible) inner structures. Note that you can also use Image>Adjust>Threshold to set thetransparency bounds.
Sometimes, the location of structures with respect to other structures in a volume is not clear. The SurfaceOpacity parameter permits the display of weighted combinations of nearest-point projection with either of the othertwo methods, often giving the observer the ability to view inner structures through translucent outer surfaces. Toenable this feature, set Surface Opacity to a value greater than zero and select either Mean Value orBrightest Point projection.
Rsb Info Nih Gov Ij Download Html Editor
Depth cues can contribute to the three-dimensional quality of projection images by giving perspective to projectedstructures. The depth-cueing parameters determine whether projected points originating near the viewer appear brighter,while points further away are dimmed linearly with distance. The trade-off for this increased realism is that datapoints shown in a depth-cued image no longer possess accurate densitometric values. Two kinds of depth-cueing areavailable: Surface Depth-Cueing and Interior Depth-Cueing. Surface Depth-Cueing works only onnearest-point projections and the nearest-point component of other projections with opacity turned on. InteriorDepth-Cueing works only on brightest-point projections. For both kinds, depth-cueing is turned off when set to zero(i.e. 100% of intensity in back to 100% of intensity in front) and is on when set at 0
Check Interpolate to generate a temporary z-scaled stack that is used to generate the projections. Z-scaling eliminates the gaps seen in projections of volumes with slice spacing greater than 1.0 pixels.This option is equivalent to using theScaleplugin from theTransformJpackage to scale the stack in the z-dimension by the slice spacing (in pixels). This checkbox is ignored if the slice spacing isless than or equal to 1.0 pixels.
Rsb Info Nih Gov Ij Download Html5
Plot Z-axis Profile
Plots the ROI selection mean gray value versus slice number. Requires a selection.Label
Adds a sequence of numbers (e.g., timestamps) and/or a label to a stack, hyperstack or virtual stack.The numbers are drawn in the current foreground color, which is set using thecolor picker (Image>Color>Color Picker).The initial XY location and font sizeare based on the existing rectangular selection, if any.Format specifies the structure of the timestamp/label:- '0': Draw unpadded numbers
- '0000': Numbers are padded with leading zeros
- '00:00': Draw minutes:seconds timestamps
- '00:00:00': Draw hours:minutes:seconds timestamps
- 'Text': Draw only the contents of the Text field
- 'Label': Displays slice labels
Text is the label to be drawn when the format is 'Text', or the stringdrawn after each number (before it if the format is '0000').
Enable Use overlay and the timestamps and/or labels willbe drawn in a non-destructive graphic overlay. Use the commands in theImage>Overlay submenu to hide, show or remove the overlay.Note that previously added overlays will be removed and virtual stackscan only have overlay labels.
Enable Use text tool font and labels will be created using the typeface and stylespecified in the Edit>Options>Fonts dialog box(example macro).
Combine
Combines two stacks (w1xh1xd1 and w2xh2xd2) to create a neww1+w2 x max(h1,h2) x max(d1,d2) stack. For example, a 256x256x40 and a 256x256x30 stack would be combined to create one 512x256x40 stack. If Combine vertically is enabled, creates a new max(w1+w2) x (h1+h2) x max(d1,d2) stack. Unused areas in the combined stack are filled with the background color.Concatenate
Concatenates two images or stacks that have the same width, height and data type.Start Animation
Animates the active stack byrepeatedly displaying its slices (frames) in sequence. Use Stop Animation, or click with the mouse, to stop. Openthe Animation Options dialog box to specify the animation speed. More than one stack can be animated at a time.As a shortcut, press the backslash key (') to start or stop animation. In ImageJ 1.38 and later, press alt plus backslashto open the Animation Options dialog.Stop Animation
Terminates animation of the active stack. As a shortcut, press the backslash key.Animation Options...
Use this dialog to set the animation speed in framesper second, set the starting and ending frame (1.38 or later), or to enable 'oscillating' animation. In ImageJ 1.38 or later, you can press alt plus backslash todisplay this dialog.Hyperstacks Submenu
This submenu contains commands that workwith hyperstacks, images that have four (4D) orfive (5D) dimensions.This is what a hyperstack looks like:Press shift-z (Image>Hyperstacks>Channels) to open the 'Channels' windowand you will be able to switch display modes (composite, color or grayscale) and enable/disable channels.
New Hyperstack...
Creates a new hyperstack. Hyperstacks have width, height, channels (c dimension),slices (z dimension) and time frames (t dimension). Check 'Label Images' in the dialog andthe channel number, slice number and frame number will be drawn on each image in the stack.Stack to Hyperstack
Converts a stack into a hyperstack. RGB stacks are convertedinto 3 channel hyperstacks.Order is the the order of the channels (C), slices (Z) and frames (T) within the stack.ImageJ hyperstacks are always in CZT order. Stacks not in CZT order will be shuffled to be in CZT order. The channel Display Mode can be Composite, Color or Grayscale.
Hyperstack to Stack
Converts a hyperstack into a stack.Reduce Dimensionality...
This command reduces the dimensionality of an hyperstack by creatinga new hyperstack with, for example, all the channels and time points at a given z positionor all the z slices for the current channel and time point.Uncheck n Channels to delete all but the current channel,n Slices to delete all but the current z slice andn Frames to delete all but the current time point. The expected dimensions and size of the reduced stack are displayed in the dialog.Check Keep Source and the original stack will not be deleted.
Channels...
Opens the 'Channels' window, or brings it to the front if it is already open. Shift-z is the keyboard shortcut forthis command.Crop
Crops the image or stack based on the currentrectangular selection. With ImageJ 1.38 or later, you can crop by pressing shift-x.Duplicate
Creates a new window containing a copy ofthe active image or rectangular selection. Hold the alt key down to skip the dialog box.Scale...
Resizes the image or selection horizontallyand/or vertically by scale factors entered into a dialog box. Check Interpolate to scale using bilinearinterpolation. Use integer scale factors (2, 3, 5, etc.) for the best looking results, particularly with graphics andtext. With scale factors less then 1.0, smoothing the source image prior to scaling may produce better looking results.Translate...
Translates (moves) the image in the x and y directions by a specified number of pixels.With stacks, you can translate either the current image or all the images in the stack.Check Preview to see how the translation will affect the image.The background at the edges of the image will be set to 0.The Align RGB Planes and Align Slice plugins on Gabriel Landini's Software pageare similar, but more interactive.
Rotate Submenu
This submenu contains commands thatrotate the active image or stack.Flip Vertical
Turns the image orselection upside down.Flip Horizontal
Replaces the image or selection witha mirror image of the original.Rotate 90 Degrees Right
Rotates the entire image orstack clockwise 90 degrees.Rotate 90 Degrees Left
Rotates the entire image orstack counter-clockwise 90 degrees.Arbitrarily...
Use this dialog to rotate the activeimage or selection clockwise the specified number of degrees.Set Grid Lines to a value greater than zero to superimposea grid on the image in preview mode.Check Interpolate to use bilinear interpolation.With 8-bit and RGB images, check Fill with Background Colorto fill with the backgound color instead of zero. Double click on the eye dropper tool toset or view the background color.Check Enlarge to Fit Result and the image will be enlargedas needed to avoid clipping.
Zoom Submenu
This submenu contains commands that control how the currentimage is displayed. The '+' and '-' keys are the preferred way touse the In and Out commands.In
Zooms in to next higher magnification level and, if possible, enlarges the window.Use the '+' key as a shortcut. Hold down the shift key to prevent the window from being enlarged.Hold down the space bar and drag to scroll the zoomed image.Double-click on the magnifying glass tool to revert to the magnificationused when the image was first opened. There are 21 possible levels (shown in title bar): 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.Out
Zooms out to next lower magnification level and, if needed, shrinks the window.Use the '-' key as a shortcut.View 100%
Displays the image using 100% magnification (1 image pixel = 1 screen pixel). Enable'Open Images at 100%' in the Edit>Options>Appearance dialog to have images automaticallyopened at 100% magnification.Original Scale
Displays the image at the magnification used when the image was first opened. As a shortcut,double click on the magnifying glass tool.To Selection
Zooms in based on the current selection.
Overlay Submenu (v1.43 and later)
This submenu contains commands for creating and working with non-destructive image overlays.An overlay consists of one or more selections. Press 'b' (Add Selection
Use the upper slider to adjust the minimum threshold value and the lower one to adjust the maximum.Hold the alt key down while adjusting the minimum to move a fixed-width thresholding window across the range of gray values. Check Dark Background if the features are lighter than the background.
Thanks to Gabriel Landini, the drop down menu on the left allows any of 16 different automatic thresholdingmethods to be selected. These methods are described on Gabriel's Auto Threshold pluginwebsite. The 'Default' method isthe modified IsoData method used by ImageJ 1.41 and earlier.
Use the drop down menu on the right to select one of three display modes. Red displays the thresholdedvalues in red. B&W switches to a mode where features are displayed in black and background in white.Over/Under displays pixels below the lower threshold value in blue, thresholded pixels in grayscale,and pixels above the upper threshold value in green.
The Auto button uses the currentlyselected thresholding method to automaticallyset the threshold levels based on an analysis of the histogram of the currentimage or selection. Apply sets thresholded pixels to black and all other pixels to white. Reset disablesthresholding and update the histogram. Click on Set to enter new threshold levels into a dialog box.
Size...
Scales the active image or selection to aspecified width and height in pixels.Check Constrain Aspect Ratio to create an image with the specified width and have ImageJ adjust the height tomaintain the original aspect ratio. Check Interpolate to use bilinear interpolation. Set New width to 0to create an image with the specified height and have ImageJ adjust the width to maintain the original aspect ratio.
Canvas Size...
Changes the canvas size of an image or stack without scaling the actual image. The width and height may be either expanded or contracted. If the canvas size is increased, then the border is filled with the current background color. Or, if Zero Fill is checked, the border is filled with pixels that have a value of zero. Use the Image>Color>Color Picker tool to change the background color. The position of the old image within the new canvas may also be specified.Show Info...
Opens a text window containinginformation about the active image. For DICOM and FITS images, also displays file header information. Use the popup menu(right-click in the Info window) to save the information to a text file or copy it to the system clipboard.Properties...
Use this command to display and set various properties of the current image or stack.The number of Channels, Slices and Frames (c, z, and t) in the image can be changed as long as the product of c, z, and tis equal to the number of images in the stack.
The Unit of Length (a string describing the measuring unit), Pixel Width, Pixel Height and Voxel Depth(all in the Unit of Length unit) can be set. The width, height and depth are automatically convertedif Unit of Length is changed from one known unit ('nm', 'um', 'micron', 'mm', 'cm', 'meter', 'km' or 'inch') to another.
With t-series stacks, the Frame Interval in seconds (reciprocal of the frame rate) can be viewed and set.Origin (always in pixels) is the reference point (0,0) of the image coordinate system.Check Global to make the current settings global (i.e., apply to all images opened during the current session).
Color Submenu
This submenu contains commands that deal with color images.Split Channels
Splits an RGB image into sepate channels (images).Also splits RGB stacks into three separate stacks.The image names have ' (red)', ' (green)' and ' (blue)' appended to them. With composite images and/or hyperstacks (e.g., the 'Organ of Corti' sample image),this command splits the stack into sepate channels.Merge Channels...
Merges 1-4 greyscale images or stacks into an RGB image or stack.Select *None* to keep a channel empty (filled with 0).Check 'Create Composite' to convert 2-4 grayscale images or stacks into a composite image or hyperstack.Check 'Keep Source Images' if you wish to keep the originals.Arrange Channels...
This command allows you to change the order of the channels in a hyperstackby entering the channel numbers in a different order.Channels that do not appear in the bottom row of thumbnail images will be deleted. Click on any thumbnail image to change that channel's color LUT.When calling this command from script or macro, you also can duplicate channels, e.g.:
Channels Tool...
Opens the 'Channels' window, or brings it to the front if it is already open.Shift-z is the keyboard shortcut for this command.Stack to RGB
Converts a two or three slice stack into an RGB image,assuming that the slices are in R, G, B order.The stack must be 8-bit or 16-bit grayscale.Also converts composite images (e.g., the HeLa Cells sample image) into RGB.Make Composite
Converts an RGB image, a 2-7 image stack or a 2-7 channel hyperstackinto a composite color image. Use the 'Channels' tool (press shift-z top open) toenable and disable the channels of a composite image. Use the 'B&C' tool(press shift-c to open) to adjust the brightness and contrast of the current channel.In the example above, all but the red and blue channels of a five channel composite image havebeen disabled using the 'Channels' tool and the 'B&C' tool is being usedto adjust the brightness and contrast of the blue channel.
Show LUT
Displays a plot of the active image's lookup table. The lookup table, or color table, describes the color that is displayed for each of the 256 possible pixel values. For 16 and32 bit images, the range of displayed pixel values is mapped to 0-255. A bar under the plot displays the color representation of the pixel values. Note that RGB color images do not use a lookup table.Edit LUT
Opens the ImageJ LUT (Lookup Table) Editor. A lookup table (LUT) in ImageJhas up to 256 entries. The entry index, and the three values (red, green and blue) associated with it,are displayed in the ImageJ status bar as you move the cursor over the LUT Editor window.Click on an entry to edit the red, green and blue values for that entry.Drag across several entries and you will be asked to define the RGB starting and ending values for theselected range. The Editor will fill the remaining entries using the selected interpolation method(Replication, Interpolation or Spline Fitting).
You can define the number of entries in the LUT usingthe 'Set' option. When increasing the number of entries, the Editor uses the specified interpolationmethod. Replication just repeats the entrieswhile Interpolation and Spline Fitting produce gradations between the colors.The 'Invert' button sets the inverse of the LUT RGB entries. 'Open' and 'Save' allow importing or exporting the LUTs.
Color Picker...
The Color Picker tool enables theuser to select foreground and background colors, which affect Edit>Fill, Edit>Draw and other color drawing commands. It displays current foreground and background colors inthe selection boxes at the bottom of the window. It has two modes:foreground and background. To change modes, click on the desiredselection box. Clicking on the Foreground/Background Switcher button sets the current foreground to the background and vice versa. The Black/White Reset button sets the foreground to black and the background to white.The color palette is based on HSB (Hue, Saturation and Brightness) color model. Hue increases as you go down the palette while saturationand brightness values are split horizontally. The left half of the palette varies onlyin brightness while the right half varies only in saturation. At thecenter of the color ramp are enlarged red, green, blue, cyan, magenta,and yellow colors for quick selection. To the left of the color palette is a grayscale ramp that goes from pure black to pure white.
Double-clicking on a color brings up the Color Selector, shown on the right inthe illustration. Use the sliders to specify the RGB values ofthe foreground or background color. To get precise colors, manually change the values in the text boxes. The title of the Color Selector window ('Foreground Color' or 'Background Color') indicates the current selection mode.
The Color Picker was written by Gali Baler, a 2003-2004 intern from Bethesda-Chevy Chase High School.
Stacks Submenu
This submenu contains commands that workwith stacks.Add Slice
Inserts a blankslice after the currently displayed slice. Hold down the alt key to add the slice before the current slice.Delete Slice
Deletes the currently displayed slice.Next Slice
Displays the slice that follows thecurrently displayed slice. As a shortcut, press the '>' key.Previous Slice
Displays the slice that precedes thecurrently displayed slice. As a shortcut, press the 'Set Slice...Displays a specified slice. The user must entera slice number greater than or equal to one and less than or equal to the number of slices in the stack.Convert Images to Stack
Creates a new stackconsisting of all images currently displayed in separate windows. Theimages must all be the same type and size.Convert Stack to Images
Converts the slices in thecurrent stack to separate image windows.Make Montage
Produces a single image which containsthe images from a stack displayed in a grid format. This can be useful for visual comparisons of a series of imagesstored in a stack. A dialog box allows you to specify the magnification level at which the images are copied, and toselect the layout of the resulting grid.With ImageJ 1.35m or later, check Use Foreground Color to draw bordersand labels in the foreground color and to fill blank areas with the background color.Use theMontage Shuffler tool macroto reorder the images in the montage.Reslice...
Reconstructs one or more orthogonal slices through the image volume represented by the current stack. A dialog allows you tospecify the spacing of the reconstructed slices.Output spacing determines the number of orthogonal slices that will reconstructed.Increasing Output spacing reduces the size of the output stack.With straight line selection, the number of orthogonal slicesgenerated is determined by the value of the 'Slice count'�field.Output spacing is ignored with line selections and one orthogonalslice is generated for each time point.
The Start at menu has four choices:
- Top - Start reconstructing slices at the top of the image
- Left - Start reconstructing at the left edge of the image
- Bottom - Start reconstructing at bottom of the image
- Right - Start reconstructing at the right edge of the image
Check Flip vertically and each slice in the output stack will be flipped vertically.Check Rotate 90 degrees and each slice in the output stack will be rotated 90 degrees.Check Avoid interpolation and no interpolation will be done.
The estimated size of the output stack and the amount of available memory are displayed at the bottom of the dialog.Increase Output Spacing to reduce the size of the output stack.
This plugin, and the ZProject plugin, were contributed by Patrick Kelly and Harvey Karten of theUniversity of California, San Diego.
ZProject...
Projects an image stack along the axis perpendicular to image plane (the so-called 'z' axis). Four different projectiontypes are supported. Average Intensity projection outputs an image wherein each pixel stores average intensityover all images in stack at corresponding pixel location. Maximum Intensity projection creates an output imageeach of whose pixels contains the maximum value over all images in the stack at the particular pixel location. SumSlices creates a real image that is is sum of the slices in the stack. Standard Deviation creates a realimage containing the standard deviation of the slices.3D Project...
Generates an animation sequence by projecting through a rotating 3D data set onto a plane. Each frame in the animationsequence is the result of projecting from a different viewing angle. To visualize this, imagine a field of parallel rayspassing through a volume containing one or more solid objects and striking a screen oriented normal to the directions ofthe rays. Each ray projects a value onto the screen, or projection plane, based on the values of points along its path.Three methods are available for calculating the projections onto this plane: nearest-point, brightest-point, andmean-value. The choice of projection method and the settings of various visualization parameters determine how bothsurface and interior structures will appear.This routine was written by Michael Castle and Janice Keller of the University of Michigan Mental Health ResearchInstitute (MHRI).
Select Nearest Point projection to produce an image of the surfaces visible from the current viewing angle. Ateach point in the projection plane, a ray passes normal to the plane through the volume. The value of the nearest nontransparent point which the ray encounters is stored in the projection image. Brightest Point projection examinespoints along the rays, projecting the brightest point encountered along each ray. This will display the brightestobjects, such as bone in a CT (computed tomographic) study. Mean Value projection, a modification ofbrightest-point projection, sums the values of all transparent points along each ray and projects their mean value. Itproduces images with softer edges and lower contrast, but can be useful when attempting to visualize objects containedwithin a structure of greater brightness (e.g. a skull).
Slice Interval is the interval, in pixels, between the slices that make up the volume. ImageJ projects the volumeonto the viewing plane at each Rotation Angle Increment, beginning with the volume rotated by InitialAngle and ending once the volume has been rotated by Total Rotation.
The Lower and Upper Transparency Bound parameters determine the transparency of structures in the volume.Projection calculations disregard points having values less than the lower threshold or greater than the upperthreshold. Setting these thresholds permits making background points (those not belonging to any structure) invisible.By setting appropriate thresholds, you can strip away layers having reasonably uniform and unique intensity values andhighlight (or make invisible) inner structures. Note that you can also use Image>Adjust>Threshold to set thetransparency bounds.
Sometimes, the location of structures with respect to other structures in a volume is not clear. The SurfaceOpacity parameter permits the display of weighted combinations of nearest-point projection with either of the othertwo methods, often giving the observer the ability to view inner structures through translucent outer surfaces. Toenable this feature, set Surface Opacity to a value greater than zero and select either Mean Value orBrightest Point projection.
Rsb Info Nih Gov Ij Download Html Editor
Depth cues can contribute to the three-dimensional quality of projection images by giving perspective to projectedstructures. The depth-cueing parameters determine whether projected points originating near the viewer appear brighter,while points further away are dimmed linearly with distance. The trade-off for this increased realism is that datapoints shown in a depth-cued image no longer possess accurate densitometric values. Two kinds of depth-cueing areavailable: Surface Depth-Cueing and Interior Depth-Cueing. Surface Depth-Cueing works only onnearest-point projections and the nearest-point component of other projections with opacity turned on. InteriorDepth-Cueing works only on brightest-point projections. For both kinds, depth-cueing is turned off when set to zero(i.e. 100% of intensity in back to 100% of intensity in front) and is on when set at 0
Check Interpolate to generate a temporary z-scaled stack that is used to generate the projections. Z-scaling eliminates the gaps seen in projections of volumes with slice spacing greater than 1.0 pixels.This option is equivalent to using theScaleplugin from theTransformJpackage to scale the stack in the z-dimension by the slice spacing (in pixels). This checkbox is ignored if the slice spacing isless than or equal to 1.0 pixels.
Rsb Info Nih Gov Ij Download Html5
Plot Z-axis Profile
Plots the ROI selection mean gray value versus slice number. Requires a selection.Label
Adds a sequence of numbers (e.g., timestamps) and/or a label to a stack, hyperstack or virtual stack.The numbers are drawn in the current foreground color, which is set using thecolor picker (Image>Color>Color Picker).The initial XY location and font sizeare based on the existing rectangular selection, if any.Format specifies the structure of the timestamp/label:- '0': Draw unpadded numbers
- '0000': Numbers are padded with leading zeros
- '00:00': Draw minutes:seconds timestamps
- '00:00:00': Draw hours:minutes:seconds timestamps
- 'Text': Draw only the contents of the Text field
- 'Label': Displays slice labels
Text is the label to be drawn when the format is 'Text', or the stringdrawn after each number (before it if the format is '0000').
Enable Use overlay and the timestamps and/or labels willbe drawn in a non-destructive graphic overlay. Use the commands in theImage>Overlay submenu to hide, show or remove the overlay.Note that previously added overlays will be removed and virtual stackscan only have overlay labels.
Enable Use text tool font and labels will be created using the typeface and stylespecified in the Edit>Options>Fonts dialog box(example macro).
Combine
Combines two stacks (w1xh1xd1 and w2xh2xd2) to create a neww1+w2 x max(h1,h2) x max(d1,d2) stack. For example, a 256x256x40 and a 256x256x30 stack would be combined to create one 512x256x40 stack. If Combine vertically is enabled, creates a new max(w1+w2) x (h1+h2) x max(d1,d2) stack. Unused areas in the combined stack are filled with the background color.Concatenate
Concatenates two images or stacks that have the same width, height and data type.Start Animation
Animates the active stack byrepeatedly displaying its slices (frames) in sequence. Use Stop Animation, or click with the mouse, to stop. Openthe Animation Options dialog box to specify the animation speed. More than one stack can be animated at a time.As a shortcut, press the backslash key (') to start or stop animation. In ImageJ 1.38 and later, press alt plus backslashto open the Animation Options dialog.Stop Animation
Terminates animation of the active stack. As a shortcut, press the backslash key.Animation Options...
Use this dialog to set the animation speed in framesper second, set the starting and ending frame (1.38 or later), or to enable 'oscillating' animation. In ImageJ 1.38 or later, you can press alt plus backslash todisplay this dialog.Hyperstacks Submenu
This submenu contains commands that workwith hyperstacks, images that have four (4D) orfive (5D) dimensions.This is what a hyperstack looks like:Press shift-z (Image>Hyperstacks>Channels) to open the 'Channels' windowand you will be able to switch display modes (composite, color or grayscale) and enable/disable channels.
New Hyperstack...
Creates a new hyperstack. Hyperstacks have width, height, channels (c dimension),slices (z dimension) and time frames (t dimension). Check 'Label Images' in the dialog andthe channel number, slice number and frame number will be drawn on each image in the stack.Stack to Hyperstack
Converts a stack into a hyperstack. RGB stacks are convertedinto 3 channel hyperstacks.Order is the the order of the channels (C), slices (Z) and frames (T) within the stack.ImageJ hyperstacks are always in CZT order. Stacks not in CZT order will be shuffled to be in CZT order. The channel Display Mode can be Composite, Color or Grayscale.
Hyperstack to Stack
Converts a hyperstack into a stack.Reduce Dimensionality...
This command reduces the dimensionality of an hyperstack by creatinga new hyperstack with, for example, all the channels and time points at a given z positionor all the z slices for the current channel and time point.Uncheck n Channels to delete all but the current channel,n Slices to delete all but the current z slice andn Frames to delete all but the current time point. The expected dimensions and size of the reduced stack are displayed in the dialog.Check Keep Source and the original stack will not be deleted.
Channels...
Opens the 'Channels' window, or brings it to the front if it is already open. Shift-z is the keyboard shortcut forthis command.Crop
Crops the image or stack based on the currentrectangular selection. With ImageJ 1.38 or later, you can crop by pressing shift-x.Duplicate
Creates a new window containing a copy ofthe active image or rectangular selection. Hold the alt key down to skip the dialog box.Scale...
Resizes the image or selection horizontallyand/or vertically by scale factors entered into a dialog box. Check Interpolate to scale using bilinearinterpolation. Use integer scale factors (2, 3, 5, etc.) for the best looking results, particularly with graphics andtext. With scale factors less then 1.0, smoothing the source image prior to scaling may produce better looking results.Translate...
Translates (moves) the image in the x and y directions by a specified number of pixels.With stacks, you can translate either the current image or all the images in the stack.Check Preview to see how the translation will affect the image.The background at the edges of the image will be set to 0.The Align RGB Planes and Align Slice plugins on Gabriel Landini's Software pageare similar, but more interactive.
Rotate Submenu
This submenu contains commands thatrotate the active image or stack.Flip Vertical
Turns the image orselection upside down.Flip Horizontal
Replaces the image or selection witha mirror image of the original.Rotate 90 Degrees Right
Rotates the entire image orstack clockwise 90 degrees.Rotate 90 Degrees Left
Rotates the entire image orstack counter-clockwise 90 degrees.Arbitrarily...
Use this dialog to rotate the activeimage or selection clockwise the specified number of degrees.Set Grid Lines to a value greater than zero to superimposea grid on the image in preview mode.Check Interpolate to use bilinear interpolation.With 8-bit and RGB images, check Fill with Background Colorto fill with the backgound color instead of zero. Double click on the eye dropper tool toset or view the background color.Check Enlarge to Fit Result and the image will be enlargedas needed to avoid clipping.
Zoom Submenu
This submenu contains commands that control how the currentimage is displayed. The '+' and '-' keys are the preferred way touse the In and Out commands.In
Zooms in to next higher magnification level and, if possible, enlarges the window.Use the '+' key as a shortcut. Hold down the shift key to prevent the window from being enlarged.Hold down the space bar and drag to scroll the zoomed image.Double-click on the magnifying glass tool to revert to the magnificationused when the image was first opened. There are 21 possible levels (shown in title bar): 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.Out
Zooms out to next lower magnification level and, if needed, shrinks the window.Use the '-' key as a shortcut.View 100%
Displays the image using 100% magnification (1 image pixel = 1 screen pixel). Enable'Open Images at 100%' in the Edit>Options>Appearance dialog to have images automaticallyopened at 100% magnification.Original Scale
Displays the image at the magnification used when the image was first opened. As a shortcut,double click on the magnifying glass tool.To Selection
Zooms in based on the current selection.
Overlay Submenu (v1.43 and later)
This submenu contains commands for creating and working with non-destructive image overlays.An overlay consists of one or more selections. Press 'b' (Add Selection) to add the current selectionto the overlay. Press shift-f (Flatten) to create an RGB image with the overlay embedded in it.The overlay is preserved when an image is saved in TIFF format.Add Selection...
Adds the current selection to the overlay. A dialog box is displayed that allows the stroke (line) color,stroke width and fill color to be set. Except for text selections, the stroke color and width areignored if a fill color is specified. Colors are specified using the name of one of the eightprimary colors (e.g., 'red', 'green', 'black') or using hex notation (e.g., '#ff0000', '#00ff00', '#000000').Non-opaque colors can be specified using 8-digit hex notation, where the first two digits specify thealpha value, for example '#800000ff' (50% blue) and '#40000000' (25% black).Add Image...
Adds an image to the overaly.Hide Overlay
Causes ImageJ to stop displaying the overlay.Show Overlay
Displays an overlay that was hidden by Hide Overlay.From ROI Manager
Creates an overlay from the selections on the ROI Manager list.To ROI Manager
Copies the selections and images in the current overlay to the ROI Manager, wherethey can be edited (moved, resized or re-colored).Remove Overlay
Permanently clears the overlay so that it cannot be restored usingShow Overlay.Flatten
Creates a new RGB image that has the overay rendered as pixel data. The RGB imageis the same size as the active image, unlikePlugins>Utilities>Grab Image, which creates a WYSIWYG (What You See Is What You Get)image that is the same size as the window.
Lookup Tables
This submenu contains a selectionof color lookup tables that can be applied to grayscale images to produce false-color images. If no image is open, a256x32 ramp image is created to display the color table. More than 100 additional lookup tables are available atrsb.info.nih.gov/ij/download/luts/. They are also available as a ZIP archive at rsb.info.nih.gov/ij/download/luts/luts.zipInvert LUT
Inverts the current lookup table. For 8-bit images, the value (v) of each entry in the table is replaced by 255-v. With inverted LUTs, pixels with a value of zero are white and pixels with a value 255 are black.Unlike the Edit>Invert command, pixels values are not altered, only the way the image is displayed on the screen.Apply LUT
Applies the current lookup table function to each pixel in the image or selectionand restores the default identity function. This modifies the gray values so that when the image is viewed using the default grayscale lookup table it will look the same as it did before. This command is equivalent to clicking on 'Apply' inImage>Adjust>Brightness/Contrast. For thresholded images, it is equivalent to clicking on 'Apply' in Image>Adjust>Threshold.
top | home | contents | previous | next
DICOM
|
