imagej.nih.gov Open in urlscan Pro
2607:f220:404:202::1:201  Public Scan

Form analysis
0 forms found in the DOM

Text Content

home | contents | previous | next


PROCESS MENU

>  * Smooth
>  * Sharpen
>  * Find Edges
>  * Find Maxima
>  * Enhance Contrast
>  * Noise>
>  * Shadows>
>  * Binary>
>  * Math>
>  * FFT>
>  * Filters>
>  * Image Calculator...
>  * Subtract Background...
>  * Repeat Command
> 
> 
> SMOOTH
> 
> Blurs the active image or selection. This filter replaces each pixel with the
> average of its 3x3 neighborhood.
> 
> 
> SHARPEN
> 
> Increases contrast and accentuates detail in the image or selection, but may
> also accentuate noise. This filter uses the following weighting factors to
> replace each pixel with a weighted average of the 3x3 neighborhood.
> 
>     -1 -1 -1
>     -1 12 -1
>     -1 -1 -1
> 
> 
> 
> FIND EDGES
> 
> Uses a Sobel edge detector to highlight sharp changes in intensity in the
> active image or selection. Two 3x3 convolution kernels (show below) are used
> to generate vertical and horizontal derivatives. The final image is produced
> by combining the two derivatives using the square root of the sum of the
> squares.
> 
>      1  2  1     1  0 -1
>      0  0  0     2  0 -2
>     -1 -2 -1     1  0 -1
> 
> 
> 
> FIND MAXIMA...
> 
> Determines the local maxima in an image and creates a binary (mask-like) image
> of the same size with the maxima, or one segmented particle per maximum,
> marked. For RGB images, maxima of luminance are selected, with the luminance
> defined as weighted or unweighted average of the colors depending on the
> Edit>Options>Conversions settings. This command is based on a plugin
> contributed by Michael Schmid.
> 
> 
> 
> A dialog box is displayed with the following options:
> 
>  * "Noise Tolerance" - Maxima are ignored if they do not stand out from the
>    surroundings by more than this value (calibrated units for calibrated
>    images). In other words, a threshold is set at the maximum value minus
>    noise tolerance and the contiguous area around the maximum above the
>    threshold is analyzed. For accepting a maximum, this area must not contain
>    any point with a value higher at than the maximum. Only one maximum within
>    this area is accepted.
>  * "Output Type" can be:
>    * "Single Points" - results in one single point per maximum
>    * "Maxima Within Tolerance" - all points within the "Noise Tolerance" for
>      each maximum
>    * "Segmented Particles" - Assumes that each maximum belongs to a particle
>      and segments the image by a watershed algorithm applied to the values of
>      the image (in contrast to Process>Binary>Watershed, which uses the
>      Euclidian distance map).
>    * "Display Point selection" - Displays a multi-point selection with a point
>      at each maximum
>    * "Count" - Displays the number of maxima in the Results window
>  * "Exclude Edge Maxima" - Excludes maxima if the area within the noise
>    tolerance surrounding a maximum touches the edge of the image (edge of the
>    selection does not matter).
>  * Check Light Background if the image background is brighter than the objects
>    you want to find, as it is in the Cell Colony image in the illustration
>    above.
>  * "Above Lower Threshold" - (This option appears for thresholded images
>    only.) Finds maxima above the lower threshold only. The upper threshold of
>    the image is ignored. If "Segmented Particles" is selected as "Output
>    Type", the area below the lower threshold is considered a background.
> 
> 
> 
> Output is a binary image, with foreground 255 and background 0, using an
> inverted or normal LUT depending on the "Black Background" option in
> Process>Binary>Options. The number of particles (as obtained by "Analyze
> Particles") in the output image does not depend on the "Output Type" selected.
> Note that "Segmented Particles" will usually result in particles touching the
> edge if "Exclude Edge Maxima" is selected. "Exclude Edge Maxima" applies to
> the maximum, not to the particle.
> 
> Find Maxima does not work on stacks, but the FindStackMaxima macro runs it on
> all the images in a stack and creates a second stack containing the output
> images. The FindMaximaRoiManager macro demonstrates how to add particles found
> by Find Maxima to the ROI Manager.
> 
> 
> ENHANCE CONTRAST
> 
> Enhances image contrast by using either histogram stretching or histogram
> equalization. Both methods are described in detail in the Hypermedia Image
> Processing Reference. Look up "enhancement" in the index.
> 
> This command does not alter pixel values as long as the Normalize and Equalize
> histogram options are not enabled.
> 
> 
> 
> Saturated pixels determines the number of pixels in the image that are allowed
> to become saturated. Increasing this value increases contrast. This value
> should be greater than zero to prevent a few outlying pixel from causing the
> histogram stretch to not work as intended.
> 
> Check Normalize and ImageJ will recalculate the pixel values of the image so
> the range is equal to the maximum range for the data type, or 0-1.0 for float
> images. The maximum range is 0-255 for 8-bit images and 0-65535 for 16-bit
> images. Note that normalization of RGB images is not supported. The Use stack
> histogram option is ignored.
> 
> With stacks another checkbox, Process all slices, is displayed. If this option
> is enabled, normalization and histogram equalization are applied to all slices
> in the stack.
> 
> Check Equalize histogram to enhance the image using histogram equalization.
> Create a selection and the equalization will be based on the histogram of the
> selection. Uses a modified algorithm that takes the square root of the
> histogram values. Hold the alt key down to use the standard histogram
> equalization algorithm. The Saturated pixels and Normalize options are ignored
> when Equalize Histogram is checked. The equalization code was contributed by
> Richard Kirk.
> 
> If Stack histogram checked, ImageJ will use the overall stack histogram
> instead of individual slice histograms, that allow optimal adjustments for
> each slice alone. This option may be especially relevant when performing
> enhancements based on a ROI.
> 
> 
> NOISE SUBMENU
> 
> Use the commands in this submenu to add noise to images or remove it. For more
> advanced capabilities, check out Erik Meijering's RandomJ package (Binomial,
> Exponential, Gamma, Gaussian, Poisson and Uniform) at
> www.imagescience.org/meijering/software/randomj/.
> 
> 
> 
> 
> 
> 
> > ADD NOISE
> > 
> > Adds random noise to the image or selection. The noise is Gaussian
> > (normally) distributed with a mean of zero and standard deviation of 25.
> > 
> > 
> > ADD MORE NOISE
> > 
> > Adds Gaussian noise with a mean of zero and standard deviation of 75.
> > 
> > 
> > SALT AND PEPPER
> > 
> > Adds salt and pepper noise to the image or selection by randomly replacing
> > 2.5% of the pixels with black pixels and 2.5% with white pixels. Note: this
> > command only works with 8-bit images.
> > 
> > 
> > DESPECKLE
> > 
> > This is a median filter. It replaces each pixel with the median value in its
> > 3 x 3 neighborhood. This is a time consuming operation because, for each
> > pixel in the selection, the nine pixels in the 3x3 neighborhood must be
> > sorted and the center pixel replaced with the median value (the fifth).
> > Median filters a good at removing salt and pepper noise.
> > 
> > 
> > REMOVE OUTLIERS
> > 
> > Replaces a pixel by the median of the pixels in the surrounding if it
> > deviates from the median by more than a certain value (the threshold).
> > Useful for correcting, e.g., hot pixels or dead pixels of a CCD image.
> > 
> > 
> > 
> > Radius determines the area used for calculating the median (uncalibrated,
> > i.e., in pixels). See Process>Filters>Show Circular Masks to see how radius
> > translates into an area. Threshold determinates by how much the pixel must
> > deviate from the median to get replaced, in raw (uncalibrated) units. Which
> > Outliers determines whether pixels brighter or darker than the surrounding
> > (the median) should be replaced.
> > 
> > 
> > REMOVE NANS
> > 
> > This filter replaces NaN (Not-a-Number) pixels in 32-bit (float) images by
> > the median of the neighbors inside the kernel area. It does not remove
> > patches of NaNs larger than the kernel size, however.
> > 
> > 
> > 
> > Radius determines the area of the circular kernel used for calculating the
> > median. The NaNs macro demonstrates how to create, count and remove NaNs.
> > Note that some ImageJ filters, such as Gaussian Blur, Mean, and Variance
> > destroy the surrounding of NaN pixel by setting it also to NaN. Other
> > filters may produce invalid results in the position of NaN pixels.
> 
> 
> SHADOWS SUBMENU
> 
> Commands in this submenu produce a shadow effect, with light appearing to come
> from a direction corresponding to the command name. The commands use
> Convolve3x3, ImageJ's 3x3 convolution function. Two of the convolution kernels
> are shown in the illustration. Shadows Demo uses all eight kernels to
> demonstrate the speed of Convolve3x3.
> 
> 
> 
> 
> 
> 
> BINARY SUBMENU
> 
> This submenu contains commands that create or process binary (black and white)
> images. They assume that objects are black and background is white unless
> "Black Background" is checked in the Process>Binary>Options dialog box.
> 
> 
> 
> 
> 
> 
> > MAKE BINARY
> > 
> > Converts an image to black and white. The threshold level is determined by
> > analysing the histogram of the current selection, or of the entire image if
> > there is no selection. The algorithm used to calculate the threshold is
> > described in the FAQs. If a threshold has been set using the
> > Image>Adjust>Threshold tool, a dialog pops up that lets you specify which
> > pixels are set to the background color and which to the foreground color,
> > and whether the background is black and the foreground is white.
> > 
> > With stacks, all images in the stack are converted to binary using the
> > calculated threshold of the currently displayed slice. Use the
> > ConvertStackToBinary macro to convert a stack to binary using locally
> > calculated thresholds. The MakeSliceBinary macro converts the current stack
> > slice to binary and advances to the next when you press a key.
> > 
> > 
> > CONVERT TO MASK
> > 
> > Converts the image to black and white based on the current threshold
> > settings (if set) or on a threshold calculated by analyzing the histogram.
> > The mask will have an inverting LUT (white is 0 and black is 255) unless
> > "Black Background" is checked in the Process>Binary>Options dialog box.
> > 
> > 
> > ERODE
> > 
> > Removes pixels from the edges of black objects. Use Process>Filters>Minimum
> > to do grayscale erosion.
> > 
> > 
> > DILATE
> > 
> > Adds pixels to the edges of black objects. Use Process>Filters>Maximum to do
> > grayscale dilation.
> > 
> > 
> > OPEN
> > 
> > Performs an erosion operation, followed by dilation. This smoothes objects
> > and removes isolated pixels.
> > 
> > 
> > CLOSE
> > 
> > Performs a dilation operation, followed by erosion. This smoothes objects
> > and fills in small holes.
> > 
> > 
> > OPTIONS...
> > 
> > Displays a dialog box that allows several settings used by commands in the
> > Binary submenu to be altered.
> > 
> > 
> > 
> > 
> > Iterations specifies the number of times erosion, dilation, opening, and
> > closing are performed.
> > 
> > Count specifies the number of adjacent background pixels necessary before a
> > pixel is removed from the edge of an object during erosion and the number of
> > adjacent foreground pixels necessary before a pixel is added to the edge of
> > an object during dilation.
> > 
> > Check Black background if the image has white objects on a black background.
> > Plugins can set this option using
> > 
> >     Prefs.blackBackground = b;
> > 
> > 
> > and macros can set it using
> > 
> >     setOption("black background", b);
> > 
> > 
> > where b is 'true' or 'false'.
> > 
> > If Pad edges when eroding is checked, Process>Binary>Erode does not erode
> > from the edges of the image. This setting also affects Process>Binary>Close,
> > which erodes from the edges unless this checkbox is selected.
> > 
> > EDM output determines the output type for the Process>Binary>Distance Map,
> > Ultimate Points and Voronoi commands. Set it to "Overwrite" for 8-bit output
> > that overwrites the input image; "8-bit", "16-bit" or "32-bit" for separate
> > output images. 32-bit output has floating point (subpixel) distance
> > resolution.
> > 
> > 
> > OUTLINE
> > 
> > Generates a one pixel wide outline of objects in a binary image.
> > 
> > 
> > SKELETONIZE
> > 
> > Repeatably removes pixels from the edges of objects in a binary image until
> > they are reduced to single pixel wide skeletons.
> > 
> > 
> > DISTANCE MAP
> > 
> > Generates a Euclidian distance map (EDM). Each foreground pixel in the
> > binary image is replaced with a gray value equal to that pixel's distance
> > from the nearest background pixel.
> > 
> > 
> > ULTIMATE POINTS
> > 
> > Generates the ultimate eroded points (UEPs) of the EDM. Requires a binary
> > image as input. The UEPs represent the centers of particles that would be
> > separated by segmentation. The UEP's gray value is equal to the radius of
> > the inscribed circle of the corresponding particle.
> > 
> > 
> > WATERSHED
> > 
> > Watershed segmentation is a way of automatically separating or cutting apart
> > particles that touch. It first calculates the Euclidian distance map (EDM)
> > and finds the ultimate eroded points (UEPs). It then dilates each of the
> > UEPs (the peaks or local maxima of the EDM) as far as possible - either
> > until the edge of the particle is reached, or the edge of the region of
> > another (growing) UEP. Watershed segmentation works best for smooth convex
> > objects that don't overlap too much.
> > 
> > 
> > 
> > Enable debugging in Edit>Options>Misc and the Watershed command will create
> > an animation that shows how the watershed algorithm works. An example is
> > available.
> > 
> > 
> > VORONOI
> > 
> > Splits the image by lines of points having equal distance to the borders of
> > the two nearest particles. Thus, the Voronoi cell of each particle includes
> > all points that are nearer to this particle than any other particle. For the
> > case of the particles being single points, this is a Voronoi tessellation
> > (also known as Dirichlet tessellation).
> > 
> > In the output, the value inside the Voronoi cells is zero; the pixel values
> > of the dividing lines between the cells are equal to the distance to the two
> > nearest particles. This is similar to a medial axis transform of the
> > background, but there are no lines in inner holes of particles. Choose the
> > output type ("Overwrite", "8-bit", "16-bit" or "32-bit") in the
> > Process>Binary>Options dialog box.
> 
> 
> MATH SUBMENU
> 
> The commands in this submenu add (subtract, multiply, etc.) a constant to each
> pixel in the active image or selection. When the result value
> overflows/underflows the legal range of the image's data type, the value is
> reset to the maximum/minimum value. With stacks, a "Process Stack?" dialog is
> displayed. This dialog has Yes (process entire stack), No (process current
> image) and Cancel buttons.
> 
> 
> > ADD...
> > 
> > Adds a constant to the image or selection. With 8-bit images, results
> > greater than 255 are set to 255. With 16-bit signed images, results greater
> > than 65,535 are set to 65,535.
> > 
> > 
> > SUBTRACT...
> > 
> > Subtracts a constant from the image or selection. With 8-bit and 16-bit
> > images, results less than 0 are set to 0.
> > 
> > 
> > MULTIPLY...
> > 
> > Multiplies the image or selection by the specified real constant. With 8-bit
> > images, results greater than 255 are set to 255. With 16-bit signed images,
> > results greater than 65,535 are set to 65,535.
> > 
> > 
> > DIVIDE...
> > 
> > Divides the image or selection by the specified real constant. Except for
> > 32-bit (float) images, attempts to divide by zero are ignored. With 32-bit
> > images, dividing by zero results in either NaN (0/0) or Infinity.
> > 
> > 
> > AND...
> > 
> > Does a bitwise AND of the image and the specified binary constant.
> > 
> > 
> > OR...
> > 
> > Does a bitwise OR of the image and the specified binary constant.
> > 
> > 
> > XOR...
> > 
> > Does a bitwise XOR of the image and the specified binary constant.
> > 
> > 
> > MIN...
> > 
> > Pixels in the image with a value less than the specified constant are
> > replaced by the constant.
> > 
> > 
> > MAX...
> > 
> > Pixels in the image with a value greater than the specified constant are
> > replaced by the constant.
> > 
> > 
> > GAMMA...
> > 
> > Applies the function f(p) = (p/255)^gamma*255 to each pixel (p) in the image
> > or selection, where 0.1 <= gamma <= 5.0. For RGB images, this function is
> > applied to all three color channels. For 16-bit images, the image min and
> > max are used for scaling instead of 255.
> > 
> > 
> > SET...
> > 
> > Fills the image or selection with the specified value.
> > 
> > 
> > LOG...
> > 
> > For 8-bit images, applies the function f(p) = log(p) * 255/log(255) to each
> > pixel (p) in the image or selection. For RGB images, this function is
> > applied to all three color channels. For 16-bit images, the image min and
> > max are used for scaling instead of 255. For float images, no scaling is
> > done. To calculate log10 of the image, multiply the result of this operation
> > by 0.4343 (1/log(10).
> > 
> > 
> > RECIPROCAL
> > 
> > Generates the reciprocal of the active image or selection. Only works with
> > 32-bit float images.
> > 
> > 
> > NAN BACKGROUND
> > 
> > Sets non-thresholded pixels in 32-bit float images to the NaN (Not a Number)
> > value. For float images, the "Apply" option in Image>Adjust Threshold runs
> > this command. Pixels with a value of Float.NaN (0f/0f),
> > Float.POSITIVE_INFINITY (1f/0f) or Float.NEGATIVE_INFINITY (-1f/0f) are
> > ignored when making measurements on 32-bit float images.
> > 
> > 
> > ABS
> > 
> > Generates the absolute value of the active image or selection. Only works
> > with 32-bit float images.
> > 
> > 
> > MACRO (EXPRESSION EVALUATOR)
> > 
> > This command performs image arithmetic using a user-specified expression. It
> > can be used to create fully-synthetic images or to perform precise pixel
> > manipulations on existing images or stacks. The MathMacroDemo macro, written
> > by Tiago Ferreira, demonstrates how to use it.
> 
> 
> FFT SUBMENU
> 
> The commands in this submenu support frequency domain display, editing and
> processing. They are based on an implementation of the 2D Fast Hartley
> Transform (FHT) contributed by Arlo Reeves, the author of the ImageFFT spinoff
> of NIH Image. For 3D FHTs, check out Bob Dougherty's 3D Fast Hartley Transform
> plugin.
> 
> 
> > FFT
> > 
> > Computes the Fourier transform and displays the power spectrum. The
> > frequency domain image is stored as 32-bit float FHT attached to the 8-bit
> > image that displays the power spectrum. Commands in this submenu, such as
> > Inverse FFT, operate on the 32-bit FHT, not on the 8-bit power spectrum. All
> > other ImageJ commands only "see" the power spectrum.
> > 
> > If the mouse is over an active frequency domain (FFT) window, its location
> > is displayed in polar coordinates. The angle is expressed in degrees, while
> > the radius is expressed in pixels per cycle (p/c). The radius is expressed
> > in [units] per cycle (e.g. mm/c) if the spatial scale of the image was
> > defined using Analyze>Set Scale. With v1.39b or later, the polar coordinates
> > of point selections are recorded by Analyze>Measure. An example is
> > available.
> > 
> > 
> > INVERSE FFT
> > 
> > Computes the inverse Fourier transform. You can filter or mask spots on the
> > transformed (frequency domain) image and do an inverse transform to produce
> > an image which only contains the frequencies selected or which suppresses
> > the frequencies selected. Use ImageJ's selection tools and fill/clear
> > commands to draw black or white areas that mask portions of the transformed
> > image. Black areas (pixel value=0) cause the corresponding frequences to be
> > filtered (removed) and white areas (pixel value=255) cause the corresponding
> > frequences to be passed. It is not, however, possible to both filter and
> > pass during the same inverse transform.
> > 
> > Note that areas to be filtered in the frequency domain image must be zero
> > filled and areas to be passed must be filled with 255. You can varify that
> > this is the case by moving the cursor over a filled area and observing that
> > the values displayed in the status bar are either 0 or 255.
> > 
> > With off-center selections, the same spatial frequency appears twice in the
> > power spectrum, at points opposite from the center. With ImageJ 1.41k and
> > later, it is sufficient to fill/clear only one of these. In the following
> > example (courtesy of Arlo Reeves), the cleared selections in the upper half
> > of the power spectrum have been automatically mirrored to the lower half, as
> > shown in the power spectrum of the filtered image.
> > 
> > 
> > 
> > The image used in this example is available at
> > rsb.info.nih.gov/ij/images/abe.tif. There is also an example that
> > demonstrates how to remove noise from images generated by a laser scanning
> > confocal microscope.
> > 
> > 
> > REDISPLAY POWER SPECTRUM
> > 
> > Recomputes the power spectrum from the frequency domain image (32-bit FHT).
> > This command allows you to start over if you mess up while editing the 8-bit
> > power spectrum image.
> > 
> > 
> > FFT OPTIONS...
> > 
> > Displays the FFT Options dialog box.
> > 
> > 
> > 
> > 
> > 
> >  * Display - These are checkboxes that specify which image(s) are created by
> >    the FFT command:
> >    * FFT Window is the standard output. It consists of an 8-bit image of the
> >      power spectrum and the actual data, which remain invisible for the
> >      user. The power spectrum image is displayed with logarithmic scaling,
> >      enhancing the visibility of components that are weakly visible. The
> >      actual data are used for the Inverse FFT command.
> >    * Raw Power Spectrum is the power spectrum without logarithmic scaling.
> >    * Fast Hartley Transform is the internal format used by the command,
> >      which is based on a Hartley transform rather than Fourier transform.
> >    * Complex Fourier Transform is a stack with two slices for the real and
> >      imaginary parts of the FFT.
> >  * Check Do Forward Transform and the current image is transformed
> >    immediately when closing the FFT Options dialog.
> > 
> > 
> > BANDPASS FILTER..
> > 
> > This is a built in version of Joachim Walter's FFT Filter plugin. It removes
> > high spatial frequencies (blurring the image) and low spatial frequencies
> > (similar to subtracting a blurred image). It can also suppress horizontal or
> > vertical stripes that were created by scanning an image line by line.
> > 
> > 
> > 
> > 
> > 
> >  * Filter Large Structures Down to - Smooth variations of the image with
> >    typical sizes of bright or dark patches larger than this value are
> >    suppressed (background).
> >    
> >    
> > 
> >  * Filter Small Structures Up to - Determines the amount of smoothing.
> >    Objects in the image smaller than this size are strongly attanuated. Note
> >    that these values are both half the spatial frequencies of the actual
> >    cutoff. The cutoff is very soft, so the bandpass will noticeably
> >    attenuate even spatial frequencies in the center of the bandpass unless
> >    the difference of the two values is large (say, more than a factor of 5
> >    or so).
> >    
> >    
> > 
> >  * Suppress Stripes - Select whether to eliminate horizontal or vertical
> >    stripes. Removal of horizontal stripes is similar to subtracting an image
> >    that is only blurred in the horizontal direction from the original.
> >    
> >    
> > 
> >  * Tolerance of Direction - This is for Suppress Stripes; higher values
> >    remove shorter stripes and/or stripes that are running under an angle
> >    with respect to the horizontal (vertical) direction.
> >    
> >    
> > 
> >  * Autoscale After Filtering puts the lowest intensity to 0 and the highest
> >    intensity to 255, preserving all intensities.
> >    
> >    
> > 
> >  * Saturate allows some intensities to go into saturation, and produces a
> >    better visual contrast. Saturate only has an effect when Autoscale is
> >    enabled.
> >    
> >    
> > 
> >  * Display Filter shows the filter generated. Note that this disables Undo
> >    of the filter operation on the original image.
> > 
> > The Bandpass Filter uses a special algorithm to reduce edge artifacts
> > (before the Fourier transform, the image is extended in size by attaching
> > mirrored copies of image parts outside the original image, thus no jumps
> > occur at the edges).
> > 
> > 
> > CUSTOM FILTER..
> > 
> > This command does fourier space filtering of the active using a
> > user-supplied image as the filter. This command does Fourier space filtering
> > of the active image using a user-supplied image as the filter. This image
> > will be converted to 8-bits. For pixels that have a value of 0, the
> > corresponding spatial frequences will be blocked. Pixel with values of 255
> > should be used for passing the respective spatial frequencies without
> > attenuation. Note that the filter should be symmetric with respect to
> > inversion of the center: Points that are opposite of the center point
> > (defined as x=width/2, y=height/2) should have the same value. Otherwise,
> > artifacts can occur.
> > 
> > For some examples, see the FFTCustomFilterDemo and FFTRemoveStreaks macros.
> > 
> > 
> > FD MATH..
> > 
> > This command correlates, convolves or deconvolves two images. It does this
> > by converting the images to the frequency domain, performing conjugate
> > multiplication, multiplication or division, then converting the result back
> > to the space domain. These three operations in the frequency domain are
> > equivalent to correlation, convolution and deconvolution in the space
> > domain. Refer to the DeconvolutionDemo and MotionBlurRemoval macros for an
> > examples.
> 
> 
> FILTERS SUBMENU
> 
> This submenu contains miscellaneous filters and plugin filters that have been
> installed by the Plugins>Utilities>Install Plugin command. For more
> information, refer to the Hypermedia Image Processing Reference at
> http://www.dai.ed.ac.uk/HIPR2/. Click on Index and look up the keywords
> convolution, Gaussian, median, mean, erode, dilate and unsharp.
> 
> 
> > CONVOLVE...
> > 
> > Does spatial convolution using a kernel entered into a text area. A kernel
> > is a matrix whose center corresponds to the source pixel and the other
> > elements correspond to neighboring pixels. The destination pixel is
> > calculated by multiplying each source pixel by its corresponding kernel
> > coefficient and adding the results. If needed, the input image is
> > effectively extended by duplicating edge pixels outward. There is no
> > arbitrary limit to the size of the kernel but it must be square and have an
> > odd width.
> > 
> > 
> > 
> > Rows in the text area must all have the same number of coefficients, the
> > rows must be terminated with a carriage return, and the coefficients must be
> > separated by one or more spaces. Kernels can be pasted into the text area
> > using the ctrl+v keyboard shortcut. Checking Normalize Kernel causes each
> > coefficient to be divided by the sum of the coefficients, preserving image
> > brightness.
> > 
> > The kernel shown is a 9 x 9 "Mexican hat", which does both smoothing and
> > edge detection in one operation. Note that kernels can be saved as a text
> > file by clicking on the "Save" button, displayed as an image using
> > File>Import>Text Image, scaled to a reasonable size using Image>Adjust>Size
> > and plotted using Analyze>Surface Plot.
> > 
> > The ConvolutionDemo macro demonstrates how to use this command in a macro.
> > 
> > 
> > GAUSSIAN BLUR...
> > 
> > This filter uses convolution with a Gaussian function for smoothing. Sigma
> > is the radius of decay to exp(-0.5) ~ 61%, i.e. the standard deviation sigma
> > of the Gaussian (this is the same as in Photoshop, but different from
> > earlier versions of ImageJ, where a value 2.5 times as much had to be
> > entered.
> > 
> > Like all ImageJ convolution operations, it assumes that out-of-image pixels
> > have a value equal to the nearest edge pixel. This gives higher weight to
> > edge pixels than pixels inside the image, and higher weight to corner pixels
> > than non-corner pixels at the edge. Thus, when smoothing with very high blur
> > radius, the output will be dominated by the edge pixels and especially the
> > corner pixels (in the extreme case, with a blur radius of e.g. 1e20, the
> > image will be raplaced by the average of the four corner pixels).
> > 
> > For increased speed, except for small blur radii, the lines (rows or columns
> > of the image) are downscaled before convolution and upscaled to their
> > original length thereafter.
> > 
> > 
> > MEDIAN...
> > 
> > Reduces noise in the active image by replacing each pixel with the median of
> > the neighboring pixel values.
> > 
> > 
> > MEAN...
> > 
> > Smooths the current image by replacing each pixel with the neighborhood
> > mean. The size of the neighborhood is specified by entering its radius in a
> > dialog box.
> > 
> > 
> > MINIMUM...
> > 
> > This filter does grayscale erosion by replacing each pixel in the image with
> > the smallest pixel value in that pixel's neighborhood.
> > 
> > 
> > MAXIMUM...
> > 
> > This filter does grayscale dilation by replacing each pixel in the image
> > with the largest pixel value in that pixel's neighborhood.
> > 
> > 
> > UNSHARP MASK...
> > 
> > Unsharp masking subtracts a blurred copy of the image and rescales the image
> > to obtain the same contrast of large (low-frequency) structures as in the
> > input image. This is equivalent to adding a high-pass filtered image and
> > thus sharpens the image. Radius is the standard deviation (blur radius) of
> > the Gaussian blur that is subtracted. Mask Weight determines the strength of
> > filtering, whereby Mask Weight=1 would be an infinite weight of the
> > high-pass filtered image that is added.
> > 
> > 
> > VARIANCE...
> > 
> > Heighlights edges in the image by replacing each pixel with the neighborhood
> > variance.
> > 
> > 
> > SHOW CIRCULAR MASKS
> > 
> > Generates a stack containing examples of the circular masks used by the
> > Median, Mean, Minimum, Maximum and Variance filters for various neighborhood
> > sizes.
> 
> 
> IMAGE CALCULATOR...
> 
> Performs arithmetic and logical operations between two images selected from
> popup menus. Image1 or both Image1 and Image2 can be stacks. If both are
> stacks, they must have the same number of slices. Image1 and Image2 must be
> the same data type but they do not have to be the same size.
> 
> 
> 
> You can select one of 12 operators from the Operation: popup menu. Check
> Create New Window and a new image or stack will be created to hold the result.
> Otherwise, the result of the operation replaces some or all of Image1. Check
> "32-bit Result" and the source images will be converted to 32-bit floating
> point before the specified operation is performed.
> 
> With 32-bit (float) images, pixels resulting from division by zero are set to
> Infinity, or to NaN (Not a Number) if a zero pixel is divided by zero. The
> divide-by-zero value can be redefined in Edit>Options>Misc.
> 
> 
> 
> Add img1 = img1+img2 Subtract img1 = img1-img2 Multiply img1 = img1*img2
> Divide img1 = img1/img2 AND img1= img1 AND img2 OR img1 = img1 OR img2 XOR
> img1 = img1 XOR img2 Min img1 = min(img1,img2) Max img1 = max(img1,img2)
> Average img1 = (img1+img2)/2 Difference img1 = |img1-img2| Copy img1 = img2
> 
> In these examples, the source and destination have inverted LUTs so zero
> pixels are white. Operations on images with non-inverted LUTs, and RGB images,
> will not produce the same results.
> 
> 
> 
> 
> 
> 
> SUBTRACT BACKGROUND...
> 
> Removes smooth continuous backgrounds from gels and other images. Based on the
> "rolling ball" algorithm described in Stanley Sternberg's article, "Biomedical
> Image Processing", IEEE Computer, January 1983. Imagine a 3D surface with the
> pixel values of the image being the height, then a ball rolling over the back
> side of the surface creates the background. The current algorithm (since
> v1.39f) uses an approximation of a paraboloid of rotation instead of a ball.
> 
> 
> 
> The Rolling Ball Radius is the radius of curvature of the paraboloid. As a
> rule of thumb, for 8-bit or RGB images it should be at least as large as the
> radius of the largest object in the image that is not part of the background.
> Larger values will also work unless the background of the image is too uneven.
> For 16-bit and 32-bit images with pixel value ranges different from 0-255, the
> radius should be inversely proportional to the pixel value range. For example,
> typical values of the radius are around 0.2 to 5 for 16-bit images (pixel
> values 0-65535).
> 
> The Light Background option allows the processing of images with bright
> background and dark objects.
> 
> With the Create Background option, the output is not the image with the
> background subtracted but rather the background itself. This option is useful
> for examining the background created (in conjunction with the Preview option).
> Create Background can be also used for custom background subtraction
> algorithms where the image is duplicated and filtered (e.g. removing "holes"
> in the background) before creating the background and finally subtracting it
> with Process>Image Calculator.
> 
> For calculating the background ("rolling the ball"), images are
> maximum-filtered (3x3 pixels) to remove outliers such as dust and then
> smoothed to reduce noise (average over 3x3 pixels). With Disable Smoothing,
> the unmodified image data are used for creating the background. Check this
> option to make sure that the image data after subtraction will never be below
> the background.
> 
> 
> 
> 
> 
> 
> REPEAT COMMAND
> 
> Reruns the previous command. The Undo and Open commands are skipped. For a
> shortcut, type shift-R.

top | home | contents | previous | next