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Use this submenu to determine the type of the active image or to convert it to another type. 8-bit?Color?Converts to 8-bit indexed color using Heckbert’s median-cut color quantization algorithm. The Process?Enhance Contrast…v command can be used to adjust the brightness and contrast of each slice in a stack, according to either the optimal for each individual slice (if Use Stack Histogram is unchecked) or the overall stack (by ticking Use Stack Histogram).
Histogram?The line graph at the top of the window, which is superimposed on the image’s histogram, shows how pixel values are mapped to 8-bit (0--255) display values. Auto?ImageJ will automatically optimize brightness and contrast based on an analysis of the image’s histogram. A run("Enhance Contrast", "saturated=0.35") macro call is generated if the command recorder (Plugin?Macro?Record…v) is running. Automatic?Automatically selects the best range given the intensity values of the image based on the percentage of the total number of pixel values from the lowest to highest pixel value.
Check Propagate to all open images to apply these values to the rest of the images currently open. With DICOM images, ImageJ sets the initial display range based on the Window Center (0028,?1050) and Window Width (0028,?1051) tags. This panel makes adjustments to the brightness and contrast of a single color of a standard RGB image (8-bit per color channel).
NB: When switching from one color to another, the changes made to one color will be lost unless Apply is clicked before.
When displayed, the intensity of each pixel that is written in the image file is converted into the grayness of that pixel on the screen. 16-bit and 32-bit grayscale images are not directly displayable on computer monitors, which typically can show only display 256?shades of gray.
It may happen that the initial windowing performed by ImageJ on these high bit--depth (or HDR[?]) images is suboptimal.
Use this tool to automatically or interactively set lower and upper threshold values, segmenting grayscale images into features of interest and background. Stack histogram? If checked, ImageJ will first compute the histogram of the whole stack (or hyperstack) and then compute the threshold based on that histogram. Auto?Uses the currently selected thresholding method to automatically set the threshold levels based on an analysis of the histogram of the current image or selection. Thresholds 24-bit RGB images based on Hue Saturation and Brightness (HSB), Red Green and Blue (RGB), CIE Lab or YUV components. Pass?If checked, values within range are thresholded and displayed (band-pass filter), otherwise, values outside the selected range are thresholded (band-reject filter). Thresholding Method?Allows any of the 16?different automatic thresholding methods to be selected (see Threshold… [T]^).
Color space?Selects the color space: HSB, RGB, CIE Lab or YUV (see Color Spaces and Color Separation^). Dark background?To be checked when features are lighter than the background (see 23: Interpreting Binary Imagesv). Original?Restores the original image and updates the buffer when switching to another image. Sample?(Experimental) Sets the ranges of the filters based on the pixel value components in a user-defined ROI. Macro?Creates a macro based on the current settings which is sent to the Macro Recorder window (Plugins?Macros?Record…v), if open. Check Constrain aspect ratio and ImageJ will adjust either the Height or the Width to maintain the original aspect ratio. Check the Average when downsizing checkbox for better results when scaling down images [19].
Opens a text window containing information about the active image (including the pixel or voxel size, since IJ?1.44k). The number of Channels (c), Slices (z) and Frames (t) in the image can be changed as long as the product of c, z, and t is equal to the number of images in the stack. Unit of Length is a string describing the measuring unit of Pixel Width, Pixel Height and Voxel Depth. With t-series stacks, the Frame Interval in seconds (reciprocal of the frame rate) can be viewed and set. Origin is the reference point 0,?0 (always in pixels) of the image coordinate system (see also Invert Y coordinatesv in Analyze?Set Measurements…v). Splits an RGB image (or stack) into three 8-bit grayscale images containing the red, green and blue components of the original. Create composite?If checked, a multi-channel composite image (see Color Composite Images^) will be created. Converts a two or three slice stack into an RGB image, assuming that the slices are in R, G, B order. Converts in place an RGB image, a 2--7 image stack or a 2--7 channel hyperstack into a composite color image. The Color Picker [17] enables the user to select foreground and background colors, which affects Edit?Fill [f]^, Draw [d]^, Clear^ and other drawing commands. The color palette is based on HSB (Hue, Saturation and Brightness) color model (see Color Spaces and Color Separation^). Double clicking on a color brings up the ColorChooser, a widget with three sliders used to specify the RGB values of the foreground or background color. Color marks are only available with color images or grayscale images that have been converted to RGB (Image?Type?^ submenu). Colored Overlays^ (see Image?Overlay?v, Overlay Brush^ tool), on the other hand, can be created on all image types becoming the easiest way to annotate grayscale images. Copy (center) and Copy (top-left)?Stack will have the width of the widest open image and the height of the highest open image. Title Contains?Enter a string into this field and ImageJ will only convert to stack images whose name contains that string. Use Title as Labels?If checked, image titles (without extension) will be used as stack labels. Produces a single grid-image containing the individual images that compose Stacks^ and 4D Hyperstacks^. Use Foreground Color?If checked, borders and labels are drawn in the foreground color and blank areas of the panel are filled with the background color.
Reconstructs one or more orthogonal slices through the image volume represented by the current stack or hyperstack [21]. The estimated size of the output stack and the amount of available memory are displayed at the bottom of the dialog.
Start at?Determines the image edge (top, left, bottom or right) from which reconstruction starts.
The intersection point of the three views follows the location of the mouse click and can be controlled by clicking and dragging in either the XY, XZ or YZ view.


Projects an image stack along the axis perpendicular to image plane (the so-called z axis) [21]. Average Intensity?projection outputs an image wherein each pixel stores average intensity over all images in stack at corresponding pixel location. Maximum Intensity?projection (MIP[?]) creates an output image each of whose pixels contains the maximum value over all images in the stack at the particular pixel location. Standard Deviation?projection creates a real image containing the standard deviation of the slices.
Median?projection outputs an image wherein each pixel stores median intensity over all images in stack at corresponding pixel location. This command creates a sequence of projections of a rotating volume (stack or hyperstack) onto a plane using nearest-point (surface), brightest-point, or mean-value projection or a weighted combination of nearest point projection with either of the other two methods (partial opacity) [40]. Each frame in the animation sequence is the result of projecting from a different viewing angle. Each ray projects a value onto the screen, or projection plane, based on the values of points along its path.
Projection Method?Select Nearest Point projection to produce an image of the surfaces visible from the current viewing angle. Opacity?Can be used to reveal hidden spatial relationships, especially on overlapping objects of different colors and dimensions. Interpolate?Check Interpolate to generate a temporary z-scaled stack that is used to generate the projections. Coordinates of the upper left corner of the selection (or the bounding rectangle for non-rectangular selections) are displayed in the graph title. The initial X,Y location, and Font size of the label are based on the existing rectangular selection, if any. Text?The string to be drawn after each number when the Format chosen is either 0 or Text (label without numeric sequence).
Use text tool font ?If checked, labels will be created using the typeface and style specified in the Fonts…^ widget.
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An attempt to perform an unsupported conversion causes a dialog box to be displayed that lists the possible conversions. With 8-bit images, brightness and contrast are changed by updating the image’s lookup table (LUT), so pixel values are unchanged.
Create a selection, and the entire image will be optimized based on an analysis of the selection. Most of times, however, the relevant image information is contained only within a narrow range of the grayscale.
With multi-channel images, the option to propagate the specified range to the remaining channels is also available. For multi-channels Stacks^ and Hyperstacks^ (Color Composite Images^) it adjusts each of the color channels independently. Use Analyze?Measure… [m]v) (with Limit to Threshold in Analyze?Set Measurements…v checked) to measure the aggregate of the selected features.
Hold Shift while adjusting the minimum to move a fixed-width thresholding window across the range of gray values. Ranges of the filters can be set manually or based on the pixel value components of a user-defined ROI. Note that the final thresholded image type is RGB, not 8-bit gray (see Image Types and Formats^). The selection is made according to the settings defined in the Process?Binary?Options…v dialog.
When applicable, other dimensions can also be resized: Depth (images) in stacks, Depth (slices) and Time (frames) in hyperstacks. Use the Channels Tool… [Z]v tool (?Shift Z?) to enable and disable the channels of a composite image. The lookup table, or color table, describes the color that is displayed for each of the 256 possible pixel values. It displays current foreground and background colors in the selection boxes at the bottom of the window.
Hue increases as you go down the palette while saturation and brightness values are split horizontally.
The title of the ColorChooser widget (Foreground Color or Background Color) indicates the current selection mode.
Foreground color can also be changed using the Color dropdown menu in the Options dialog of drawing tools such as Arrow^, Brush^, Overlay Brush^ and Pencil^ tools. Operations specifically related to Hyperstacks^ are listed in the Image?Hyperstacks?v submenu. The user must enter a slice number greater than or equal to one and less than or equal to the number of slices in the stack. Smaller images will then be copied (either to the center or to the upper left corner) of the slice. As described in Stacks?Tools?Remove Slice Labelsv, these labels (up to 60 characters) correspond to the image subtitle, the line of information above the image.
Slice labels (up to 60 characters) correspond to the image subtitle, the line of information above the image.
With hyperstacks, the projection is performed on the active time frame, or for all time points if All Time Frames is checked. The user may choose to rotate the volume about any of the three orthogonal axes (x, y, or z), make portions of the volume transparent (using thresholding), or add a greater degree of visual realism by employing depth cues. To visualize this, imagine a field of parallel rays passing through a volume containing one or more solid objects and striking a screen oriented normal to the directions of the rays.
Three methods are available for calculating the projections onto this plane: nearest-point, brightest-point, and mean-value. At each point in the projection plane, a ray passes normal to the plane through the volume. ImageJ projects the volume onto the viewing plane at each Rotation Angle Increment, beginning with the volume rotated by Initial Angle and ending once the volume has been rotated by Total Rotation. Projection calculations disregard points having values less than the lower threshold or greater than the upper threshold. The (surface) Opacity parameter permits the display of weighted combinations of nearest-point projection with either of the other two methods, often giving the observer the ability to view inner structures through translucent outer surfaces. The depth-cueing parameters determine whether projected points originating near the viewer appear brighter, while points further away are dimmed linearly with distance. Z-scaling eliminates the gaps seen in projections of volumes with slice spacing greater than 1.0?pixels. Photo torrent album corelcorwel wedding, titles can easily free-your ordinary flash with gallery favorite free May 18, 2009-4 min-Uploaded by shapecollageDownload Shape Collage at http: www Shapecollage. With 16-bit and 32-bit images, the display is updated by changing the mapping from pixel values to 8-bit display values, so pixel pixel values are also unchanged.
The optimization is done by allowing a small percentage of pixels in the image to become saturated (displayed as black or white).


Press H (Analyze?Histogram [h]v) and you will see that the minimum pixel value in the image is -719 and the maximum is 1402.
The window defines the range of gray values that are displayed: values below the window are made black, while values above the window are white. This command, implemented in version?1.43l, is an experimental built-in version of the Threshold Colour plugin [20] and is not yet fully integrated into ImageJ. The implementation of the bicubic method (Catmull-Rom interpolation) is derived from Burger and Burge, 2008 [104].
If the canvas size is increased, the border is filled with the current background color (see Color Picker… [K]v), or, if Zero Fill is checked, the border is filled with pixels that have a value of zero. 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. When creating composite images, original LUTs and display ranges are preserved unless Ignore source LUTs is checked.
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.
Color Choosers are evoked by double clicking on a color of the CP window and can be used to retrieve Hexadecimal Color Valuesv. The left half of the palette varies only in brightness while the right half varies only in saturation. A dialog box allows you to specify the magnification level at which the images are copied, and to select the layout of the resulting grid. With lines selections, a stack is created by shifting (by Output spacing) the line down and to the left to generate additional slices for the output stack.
The choice of projection method and the settings of various visualization parameters determine how both surface and interior structures will appear. The value of the nearest non transparent point which the ray encounters is stored in the projection image.
Setting these thresholds permits making background points (those not belonging to any structure) invisible. To enable this feature, set Opacity to a value greater than zero and select either Mean Value or Brightest Point projection. The trade-off for this increased realism is that data points shown in a depth-cued image no longer possess accurate densitometric values. This option is equivalent to using the Scale plugin from the TransformJ package to scale the stack in the z-dimension by the slice spacing (in pixels). Com Shape Collage is an automatic Shape Collage is a free online photo collage maker software program. ImageJ displays images by linearly mapping pixel values in the display range to display values in the range 0--255. Each additional click on Auto increases the number of saturated pixels and thus the amount of optimization. The Set Display Range dialog allows you to choose how to scale the range of gray levels of 16-bit images. Note that these are global thresholding methods that typically cannot deal with unevenly illuminated images (such as in brightfield microscopy).
Click on an entry to edit the red, green and blue values for that entry using a Color Selector window (cf.
At the center of the color ramp are enlarged red, green, blue, cyan, magenta, and yellow colors for quick selection. The hex value of the final color is also displayed, offering a convenient way to retrieve custom colors to, e,g, personalize Overlays^ (see 20: Hexadecimal Color Valuesv).
If no slice metadata exists (the setMetadata() macro function can be used to customize slice labels) images are labelled with slice numbers. Brightest Point projection examines points along the rays, projecting the brightest point encountered along each ray. By setting appropriate thresholds, you can strip away layers having reasonably uniform and unique intensity values and highlight (or make invisible) inner structures.
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Pixels with a value less than the minimum are displayed as black and those with a value greater than the maximum are displayed as white.
In these cases, local algorithms are more appropriated, by allowing the threshold to smoothly vary across the image.. Foreground color is also reflected in drawing tools such as the Arrow^, Brush^, Flood Filler^ and Pencil^ tools.
To the left of the color palette is a grayscale ramp that goes from pure black to pure white.
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