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auto_local_threshold

auto_threshold

ij-align_4

ImageJ plugin to align interactively up to 4 images

ij-align_rgb_planes

This plugin An ImageJ plugin to shift (move in the x and y directions), stretch and rotate the red green and blue planes in an RGB image.

ij-align_slice

This is an ImageJ plugin to manually shift (move in the x and y directions) stretch and rotate a particular slice in an image stack.

ij-anaglyph

Creates colour or greyscale, red-cyan or red-green anaglyphs, stereo pairs (crossed view stereo pairs) and depth-map images from the depth data and focused image generated with the extended depth of field plugin (http://bigwww.epfl.ch/demo/edf/index.html).

ij-auto_threshold_auto_local_threshold

Two ImageJ plugins to binarise images using a variety of methods. This is not necessary to Fiji. The Auto_Local_Threshold is probably already distributed with ImageJ, See: https://blog.bham.ac.uk/intellimic/g-landini-software/ and https://blog.bham.ac.uk/intellimic/g-landini-software/auto-threshold-and-auto-local-threshold/

ij-blend

ImageJ plugin to blend (linearly) two greyscale or RGB images with a chosen mix ratio. See: https://blog.bham.ac.uk/intellimic/g-landini-software/

ij-colour_correct

ImageJ plugin to "correct" the colours of an image by first subtracting the mean RGB values of a number of selected points considered to be 'black' and then subtracts the background by performing the ratio of the image and the mean RGB values of a number of points considered to be 'white' minus the 'black'. It does not correct for uneven illumination. See: https://blog.bham.ac.uk/intellimic/g-landini-software/

ij-colour_deconvolution2

The Colour Deconvolution 2 ImageJ plugin implements stain unmixing with Ruifrok and Johnston’s method described in [Ruifrok AC, Johnston DA. Quantification of histochemical staining by color deconvolution. Analytical and Quantitative Cytology and Histology 23: 291-299, 2001]. The technique is useful to unmix dyes in images where colours mix subtractively (bright field microscopy using histological stains, watercolours or printed material using transparent inks). It is not suitable for fluorescence microscopy (fluorophores mix additively) or reflectance images. The code is based on a NIH Image macro kindly provided by A. C. Ruifrok with additional modifications. See the source code for the version history and contributors.

ij-convex_hull_plus

An ImageJ plugin to compute the convex hull and the minimum bounding circlte of a binary set.

ij-dichromacy

This plugin simulates the three main types dichromatic vision due to lack of function or absence of retinal photosensitive pigments: protanopia (red), deuteranopia (green) and tritanopia (blue cones deficiency).

ij-ij_robot

An ImageJ plugin that calls the Robot Java class to allow the macro language controlling other programs via programmed clicking and key presses.

ij-isophotcontour

These plugins take a greyscale image and create a new image [called IsoPhot] with up to 8 contour lines in the grey scale range. Isophotcontour2 can be drawn in different selected colours and depth levels.

ij-list_luts

This ImageJ plugin then opens every LUT file in the selected directory and creates a new RGB stack (automatically saved as LUTs.tif in the "/plugins" folder) consisting of a LUT strip and (if selected) the name in each slice (the LUT name and the LUT values are also stored as metadata in each slice of the stack).

ij-morphology

Collection of ImageJ plugin for Mathematical Morphology

ij-rcc8d

a set of ImageJ/Fiji plugins to perform spatial reasoning using the region connection calculus (RCC) between two regions embedded in two images. Please see: https://blog.bham.ac.uk/intellimic/spatial-reasoning-with-imagej-using-the-region-connection-calculus/

ij-results_histogram

This ImageJ plugin creates a histogram from a selected column of the Results Table data. Note that not everything that is shown in the Results window is necessarily in the Results Table. This was incorporated into ImageJ 1.35g as the Analyze>Distribution... command.

ij-retinex

This is an implementation of the Retinex filter from the GIMP package. Retinex filtering is based on Land's theory of image perception. Several algorithms exist and among these the multiscale retinex with colour restoration algorithm (MSRCR) combines colour constancy with local contrast enhancement so images are rendered in a similar way to the colour perception of the human vision. plugin was written by Francisco Jiménez Hernández (UAEMex) during a research visit to Birmingham University, School of Dentistry.

ij-threepointcircularroi

This ImageJ plugin creates a circular ROI based on 3 user selected points on an image. The log window reports the coordinates of the centre of the circle and its radius. Co-linear points (that define an impossible circle) return a radius of -1.

ij-threshold_colour

This plugin (a modification of Bob Dougherty's BandPass2 filter) allows to threshold a colour RGB images in the HSB, RGB, CIE Lab and YUV spaces. It supports extracting the range of HSB, RGB, CIE Lab or YUV values from a sample ROI (any type). Use: Extract the files from the zip archive and put them somewhere in the plugins directory (or subdirectory). The Threshold_Colour entry will appear in the Plugins hierarchy, depending on the subdirectory which the plugin is copied to.

list-of-update-sites

The update sites ImageJ knows about automatically