Utility Plugins

The GDSC plugins provide various utility tools for image analysis. The following tools are available:

Binary Image Processing

Threshold Provides methods to threshold an image into foreground and background pixels. This is a modified version of the Auto Threshold plugin developed by Gabriel Landini. An additional method had been added that sets the threshold as the image average plus a factor of the standard deviation. This is a fast method that can be used within the Find Peaks algorithm
Multi Threshold Thresholds an image into levels using multiple thresholds. Based on the Multi Threshold plugin developed by Yasunari Tosa; the modifications allow processing 16-bit images and further output options
Mask Creater Creates a mask from an image with the following options:
  • Use as mask: any non-zero pixel
  • Min Display Value: any pixel above the minimum displayed value (set using Image > Adjust > Brightness/Contrast). This respects the display value for each channel
  • Use ROI: any pixel inside the marked ROI
  • Threshold: perform thresholding (z-stack planes from the same time point are thresholded collectively)
The plugin can operate on stacks and optionally can extract a specified frame, slice or channel to create the mask.
Edge Mask Create an edge mask from an image. Edges are defined where the gradient is steepest. Optionally allows: the edge lines to be pruned to leave only closed loops; and filling of loops to create a mask.

Requires the imagescience.jar file from the FeatureJ package.
Apply Mask Create a mask from a source image using the Mask Creater and apply it to a target image. All pixels outside the mask in the target image will be set to zero.
Skeleton Analyser Skeletonise (reduce to single pixel lines) a mask image. Then produce a set of lines connecting node points on the skeleton.
Thread Analyser Analyses an image using a given mask. Skeletonises the mask image and extracts a set of lines connecting node points on the skeleton. Output statistics about each of the lines using the original image and the Euclidian Distance Map (EDM) of the mask.

Other Tools

Contrast Enhancer Runs the ImageJ contrast enhancer (see Image > Adjust > Brightness/Contrast) on all the open images. This allows a one-click adjustment of all the open images for optimal viewing
Difference of Gaussians Performs a Difference of Gaussians filter for local contrast enhancement. The filter performs subtraction of one blurred version of an image from another, less blurred version of the original. The result is an image containing only the information contained within the spatial frequency between the two blurred images.
Align Images Aligns an image stack to a reference image using XY translation to maximise the normalised correlation. Outputs a new stack with the best alignment with optional sub-pixel accuracy (performed using a Gaussian fit or Cubic spline fit).

Contains options to: restrict the translation space; provide a mask image to specify which pixels to include in the analysis; and clip the bicubic interpolated output to fit within the min-max of the original image.
Align Images FFT Aligns an image stack to a reference image using XY translation to maximise the normalised correlation. The correlation is computed in the Frequency domain using Fast Fourier Transforms. Edge artifacts of the Frequency domain are reduced by using a window function on the image (gradually reducing the edge pixels to zero).

Outputs a new stack with the best alignment with optional sub-pixel accuracy (performed using a Gaussian fit or Cubic spline fit).

Contains options to restrict the translation space.

Note: This plugin is faster than the 'Align Images' plugin for large images and/or a large translation space. Note that the results will differ slightly due to the use of different correlation methods.
Align Stacks Aligns open image stacks to a reference image using XY translation to maximise the normalised correlation. Accepts multi-dimensional stacks. The self-align mode aligns all timepoints within a stack to the current frame.

For each timepoint a maximum/average intensity projection is performed per channel. The projection is thresholded to extract the signal, normalised to 0-255 and the resulting channel images are tiled to a composite image. The composite is then aligned using the maximum correlation between the images. Using a composite ensures each channel contributes equally to the aligment. The translation is applied to the entire stack for that timepoint.
Image Scaler Scales all images in a stack so that the maximum of the image is set to the specified value. For example this can be used to scale a floating point image so that the maximum is 255 for correct display.

Can accept a list file of images allowing a set of images to be scaled together. The maximum of the entire set of images is used to calculate the scale factor applied to each image.
Cell Outliner Find cell edges using marked seed points. Best suited to identify round cells with edge pixels either lighter or darker than the cell.

For each point ROI the plugin uses a curved edge filter to find edges within a range of an expected radius. The minimum/maximum size is set using the radius +/- tolerance. Edge detection is performed using an approximation to the Laplacian-of-Gaussian (LoG) and the kernel size and smoothing can be controlled.

The edge detection is weighted using the distance to the current outline of the cell (initially a circle of the specified radius around the point). A polygon outline is constructed using the highest edge value in each 10 degree segment around the centre. This is fitted using an oval shape of two ellipses back-to-back and the process iterated using the new cell outline. The final outline can be output as the polygon shape or the elliptical fit. This can be dilated to expand the outline to encompass the entire cell.

Supports a preview allowing the parameters to be interactively set. The final call produces a mask image and options are provided to process each plane/frame of a hyperstack.
Spot Analyser Identifies particles (e.g. cells) using thresholding and excludes small particles based on pixel count. The average intensity of each channel inside and outside the spot are then compared for the top N spots to identify increases in signal within spot regions.
HSB Picker Installs a tool into the menu that allows Hue-Saturation-Brightness (HSB) values to be sampled from an RGB image by mouse click. Pixels are sampled using a radius around the clicked position. The average HSB values and the standard deviations from all sampled pixels are shown in a frame.

Provides the ability to call the HSB Filter. The filter values are set using the averages and the widths using the scaled standard deviations (e.g. av +/- scale * std.dev.).
HSB Filter Provides the ability to filter pixels in an RGB image using Hue-Saturation-Brightness (HSB) values. All pixels not within the specified width of the given values are set to zero.

Note that Hue is a continuous property where values are wrapped around from 1 to 0.
Spot Separation Finds spots in an image. Locates the closest neighbour spot within a radius and produces a line profile through the spots. If no neighbour is present produces a line profile through the principle axis. Outputs the separation between the spot maxima to a table.

Allows analysis of regions using the ROI selection tools and respects manual thresholding to identify spots.
Z-Project2... Extends the ImageJ Z-Project command to add the a 'Mode' projection option. The mode can be calculated with or without ignoring zero values.

This plugin is useful for projecting 3D masks, for example those created by the FindFoci plugin.
Intensity Analysis Analyses the mean value within an ROI across a stack of exposures. Exposures must be set within the slice labels. Saturated pixels within an ROI remove that slice from analysis. A linear fit is made of the mean verses exposure using a rolling window and the gradient reported for the best fit. The gradient is a measure of the pixel intensity within the ROI.

This plugin assumes images are taken of the same object at different exposure times on a camera with a linear response curve. Thus doubling the exposure should double the pixel value. The plugin allows analysis of images with a large dynamic range by capturing each object with a suitable exposure. Drift should be minimal for the best results.
Measure 3D Installs a tool into the menu that allows distances to be measured in 3D. Distance is measured between two successive mouse clicks on the same channel and time frame of an image. Results are recorded to a table.

Download the plugin.

For further details on GDSC ImageJ plugins please contact Alex Herbert.