Imagej threshold binary options

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Generates the absolute value of the active image or selection. Works only with bit float or signed bit image images. This command performs image arithmetic using an expression specified by the user [ 32 ]. It can be used to create fully-synthetic images or to perform precise pixel manipulations on existing images. The MathMacroDemo macro demonstrates the usage of this command.

Expression plugin. The commands in this submenu support frequency domain display, editing and processing. The frequency domain image is stored as bit float FHT attached to the 8-bit image that displays the power spectrum. Computes the Fourier transform [? If the mouse is over an active frequency domain FFT window, its location is displayed in polar coordinates.

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. 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 You can verify 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 With off-center selections, the same spatial frequency appears twice in the power spectrum, at points opposite from the center. Recomputes the power spectrum from the frequency domain image bit FHT.

This command allows you to start over after mis-editing the 8-bit power spectrum image. Displays the FFT Options dialog box. 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. 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 [ 33 ]. Objects in the image smaller than this size are strongly attenuated. 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. Removal of horizontal stripes is similar to subtracting an image that is only blurred in the horizontal direction from the original.

Note that this disables Undo of the filter operation on the original image. This command does Fourier space filtering of the active image using a user-supplied spatial domain non-FFT image as the filter. This image will be converted to 8-bit. For pixels that have a value of 0, the corresponding spatial frequencies will be blocked. Pixel with values of should be used for passing the respective spatial frequencies without attenuation.

Otherwise, artifacts can occur. This command correlates, convolves or deconvolves two images. More information on image filters can be obtained by looking up related keywords convolution, Gaussian, median, mean, erode, dilate, unsharp , etc.

Does spatial convolution using a kernel entered into a text area. 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 Ctrl V. Checking Normalize Kernel causes each coefficient to be divided by the sum of the coefficients, preserving image brightness.

ConvolutionDemo macro. This filter uses convolution with a Gaussian function for smoothing [ 37 ]. 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. 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. This command calculates a three dimensional 3D gaussian lowpass filter using a 3-D Gaussian. Gaussian Blur 3D source code. Reduces noise in the active image by replacing each pixel with the median of the neighboring pixel values.

Smooths the current image by replacing each pixel with the neighborhood mean. Sharpens and enhances edges by subtracting a blurred version of the image the unsharp mask from the original. Increasing the Gaussian blur radius will increase contrast. Increasing the Mask Weight value will provide additional edge enhancement. Highlights edges in the image by replacing each pixel with the neighborhood variance.

This submenu allows the execution of commands in a series of images without manual intervention. Nevertheless a directory hierarchy can be transversed using ImageJ macro language cf. BatchProcessFolders macro. Three critical aspects to keep in mind when performing batch operations that modify processed images:.

Note that measurements are performed on non thresholded images. Selects the source folder containing the images to be processed. Selects the destination folder where the processed images will be stored. For better results, Average when downsizing is automatically selected when scaling down images. Runs a macro over a specified folder. Note that original files will not be saved if this field is left empty.

Previously written macros can be imported using Open … When editing the macro beware of any statements that may interfere with the normal operation of the batch processor such as Close or Open calls. Image1 or both Image1 and Image2 can be stacks. If both are stacks, they must have the same number of slices. Image1 and Image2 do not have to be the same data type or the same size. With 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.

If unchecked, the result of the operation is applied directly to Image1. Calculator Plus plugin. Removes smooth continuous backgrounds from gels and other images [ 39 ]. Imagine that the 2D grayscale image has a third dimension height by the image value at every point in the image, creating a surface.

A ball of given radius is rolled over the bottom side of this surface; the hull of the volume reachable by the ball is the background to be subtracted. Rolling ball radius should be set to at least the size of the largest object that is not part of the background. 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 bit and bit images with pixel value ranges different from , the radius should be inversely proportional to the pixel value range e. 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. With Disable Smoothing checked, 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. How to correct background illumination in brightfield microscopy by G. Reruns the previous command. Points at maxima Multi-point selection. Segmentation Movie. Power spectrum with mask that filters low frequencies. Result of inverse transform. Power spectrum with mask that passes low frequencies. Edited power spectrum. Inverse transform. Power spectrum after filtering.

Source image img 1 :. The binary will not be created at all? The macro is developed for image analysis. The macro has been working until fiji was uninstalled then reinstalled and now does not work. The raw image, turns red and white after thresholding and one binary; and white after the second binary. This second binary is not working. The convert to mask function appears to sometimes work instead. This second binary conversion to white image is necessary for the binary connectivity plugin.

Below is the section of the macro that appears to be responsible. Although i suspect the issue is due to default settings around the make binary or thresholding of the image. Hm when I execute the macro snippet in a fresh copy of Fiji on ubuntu I get a binary image with one of the samples images using the Huang threshold.

Above is a link with the image. The settings is a good thought and i will have to get in touch with my co-workers for the correct default settings. I really think there is a mixup in the background foreground color settings either under Options or Binary options. I usually have such issues due to changed settings there or some settings silently assumed by the macro.

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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. This option cannot be used when finding minima image with light background and inverted LUT. 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. Enhances image contrast by using either histogram stretching or histogram equalization. Both methods are described in detail in the Hypermedia Image Processing Reference [?

Increasing this value will increase contrast. This value should be greater than zero to prevent a few outlying pixel from causing the histogram stretch to not work as intended. The maximum range is for 8-bit images and for bit images. With stacks another checkbox , Normalize All n Slices , is displayed. If checked, normalization will be applied to all slices in the stack. Create a selection and the equalization will be based on the histogram of that selection. Uses a modified algorithm that takes the square root of the histogram values.

Hold Alt to use the standard histogram equalization algorithm. This option may be specially relevant when performing enhancements based on a ROI. Use the commands in this submenu to add noise to images or remove it. Adds random noise to the image or selection. The noise is Gaussian normally distributed with a mean of zero and standard deviation of Adds Gaussian noise with a mean of zero and a chosen standard deviation.

Adds salt and pepper noise to the image or selection by randomly replacing 2. This command only works with 8-bit images. This is a median filter. Median filters are good at removing salt and pepper noise. 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. This filter replaces NaN Not-a-Number pixels in bit float images by the median of the neighbors inside the circular kernel area defined by Radius [ 31 ].

It does not remove patches of NaNs larger than the kernel size, however. Other filters may produce invalid results in the position of NaN pixels. Commands in this submenu produce a shadow effect, with light appearing to come from a direction corresponding to the command name East , North , Northeast , Northwest , South , Southeast , Southwest and West.

The illustration below shows four of the Shadows convolution kernels. This submenu contains commands that create or process binary black and white images. Converts an image to black and white. Removes pixels from the edges of objects in a binary image. Adds pixels to the edges of objects in a binary image. Performs an erosion operation, followed by dilation. This smoothes objects and removes isolated pixels.

Performs a dilation operation, followed by erosion. This smoothes objects and fills in small holes. Generates a one pixel wide outline of foreground objects in a binary image. The line is drawn inside the object, i. This command fills holes connected background elements in objects by filling the background [ 34 ]. Repeatably remove pixels from the edges of objects in a binary image until they are reduced to single-pixel-wide shapes topological skeletons.

ImageJ implements a thinning algorithm from Zhang and Suen. A fast parallel algorithm for thinning digital patterns. The algorithm calculates the index number for each object pixel, and uses the lookup table to decide if the pixel is eliminable. This process is repeated until no pixel can be eliminated. AnalyzeSkeleton plugin, BinaryProcessor source code. Topographic skeletons can be analyzed using the AnalyzeSkeleton plugin. Generates a Euclidian distance map EDM from a binary image [ 38 ].

Generates the ultimate eroded points UEPs [? In the output, the points are assigned the EDM value, which is equal to the radius of the largest circle that fits into the binary particle, with the UEP as the center. Watershed segmentation is a way of automatically separating or cutting apart particles that touch.

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 touches a region of another growing UEP. 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. When particles are single points, this process 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 between 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. Iterations can be aborted by pressing Esc. This option is only available when the active image is binary. This means object s will be inferred on a image-per-image basis.

The commands in this submenu add subtract, multiply, etc. With stacks, the dialog depicted on the left is displayed. Adds a constant to the image or selection. With 8-bit images, results greater than are set to With bit signed images, results greater than 65, are set to 65, Subtracts a constant from the image or selection.

With 8-bit and bit images, results less than 0 are set to 0. Multiplies the image or selection by the specified real constant. Divides the image or selection by the specified real constant. Except for bit float images, attempts to divide by zero are ignored. Pixels in the image with a value less than the specified constant are replaced by the constant. Pixels in the image with a value greater than the specified constant are replaced by the constant. For RGB images, this function is applied to all three color channels.

For bit images, the image min and max are used for scaling instead of GammaCorrectionTool macro. For float images, no scaling is done. To calculate log 10 of the image, multiply the result of this operation by 0.

Sets non-thresholded pixels in bit float images to the NaN Not a Number value. Pixels with a value of Float. Generates the absolute value of the active image or selection. Works only with bit float or signed bit image images. This command performs image arithmetic using an expression specified by the user [ 32 ]. It can be used to create fully-synthetic images or to perform precise pixel manipulations on existing images. The MathMacroDemo macro demonstrates the usage of this command.

Expression plugin. The commands in this submenu support frequency domain display, editing and processing. The frequency domain image is stored as bit float FHT attached to the 8-bit image that displays the power spectrum. Computes the Fourier transform [? If the mouse is over an active frequency domain FFT window, its location is displayed in polar coordinates.

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. 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. 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.

Light Background - Allows the processing images that have light background and dark objects. 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.

This option only works when finding maxima of the pixel value in the mathematical sense, i. Preview Point Selection - Shows the maxima with the current parameters as a multi-point selection superimposed on the image. If this option is checked, the number of maxima found is also displayed in the dialog box. 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 applied to a noisy image with different options Exclude Edge Maxima selected. 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. With binary images, removes pixels from the edges of black objects. With binary images, adds pixels to the edges of black objects.

Performs an erosion operation, followed by dilation. With binary images, this smooths objects and removes isolated pixels. Performs a dilation operation, followed by erosion. With binary images, this smooths objects and fills in small holes. Display 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.

Set it to overwrite for 8-bit output that overwrites the input image; 8-bit , bit or bit for separate output images. Generates a one pixel wide outline of foreground black objects in a binary image. The line is drawn inside the object, i. Repeatably removes pixels from the edges of objects in a binary image until they are reduced to single pixel wide skeletons. Objects are assumed to be black and background white.

Note that there exist many skeletonizing algorithms. 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. 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.