Java

View your multi-channel data as a montage with one image per channel plus a merged, color channel (useful to create figures for communication). 

This viewer plugin will split all N channels of the active sequence into a montage of N+1 images, with one image for each channel, plus an additionnal color (merge) rendering.

Image segmentation by representative colors selection. Two versions are available :

• thresholding
• positive and negative colors selection and SVM learning

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Coloc 2 is Fiji's plugin for colocalization analysis. It implements and performs the pixel intensity correlation over space methods of Pearson, Manders, Costes, Li and more, for scatterplots, analysis, automatic thresholding and statistical significance testing.

Coloc 2 does NOT perform object based colocalization measurements, where objects are first segmented from the image, then their spatial relationships like overlap etc. are measured. This complementary approach is implemented in many ways elsewhere.

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Saves a RGB image (typically a screenshot) into a CMYK TIFF (required by publishers for high-fidelity color printing).

Wavelet Spot Detector for Blocks, to integrate in Icy protocols.

The swiss army knife of plugin developers. Automatically generates elegant graphical interfaces with rich and intuitive user interaction based on your algorithm’s parameters.

Fills holes below a given threshold. 3D data is currently processed slice per slice.

Fills the holes in all the ROI of the active sequence (also works in Protocols).

This plugin copies the pixel size from the calibration of one image or stack to a second image or stack. This allows one to copy the spatial calibration from one stack to another.

A second dialog allows to enter the scale factors.

This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and that of the background. Works on both binary and gray-scale data. Output can be pushed to the swimming pool for other plug-ins to further exploit the extracted objects.

Plugin designed to allow easy semi-automatic tracing of neurons or other filament-like structures (e.g., microtubules, blood vessels) through either 2D images or 3D image stacks. Data can be imported and exported in SWC files for interaction with other software, or details of the traces can be exported as CSV files for analysis in spreadsheets or statistical software.

This plugin is included in Fiji by default.

This plugin allows to open images embedded in PDFs.

This plugin parses arbitrary mathematical expressions and compute results using images as variables.

• Counts the number of 3D objects in a stack.
• quantifies for each found object the following parameters:
  • 3D intensity related measurement (with possible redirection to an image with the actual intensity value to be measured, for example for two channels measurements)
  • Volume and shape factors measurements, surface etc...
• generates results representations such as:
  • Objects' map;
  • Surface voxels' map;
  • Centroids' map;
  • Centres of masses' map.

As ImageJ's “Analyze Particles” function, 3D-OC also has a “redirect to” option, allowing one image to be taken as a mask to quantify intensity related parameters on a second image. But unlike the Analyze particle, it include a thresholding option, meaning that you can start from a gray level  stack, not necessarily a binary mask.

To use it, first set the list of measurements by editing 3D OC Options. Both (3D Object counter and 3D OC Options are now in the default Fiji "Analyze" menu.

Add some noise with customizable characteristics (Gaussian noise, Poisson noise, salt & pepper, etc.) to a sequence. ICY plugin.

Layer for 3D View that displays a Bounding Box around the object.

The fractional splines are an extension of the polynomial splines for all fractional degrees α > -1. Their basic constituents are piecewise power functions of degree α. One constructs the corresponding B-splines through a localization process similar to the classical one, replacing finite differences by fractional differences. The fractional B-splines share virtually all the properties of the classical B-splines, including the two-scale relation, and can therefore be used to define new wavelet bases with a continuously-varying order parameter

The smoothing is applied by the way of a bi-exponential filter, itself realized by a pair of one-tap recursions. It is therefore very fast; moreover, its computational cost is truly independent of the amount of smoothing. Meanwhile, the preservation of edges is obtained by a range filter akin to the range filter found in a bilateral filter. More technical details are available here.

The plugin allows one to control the amount of smoothing, the type of range filter, its broadness, and to iterate the filter several times if desired. We illustrate in Figure 2 a possible outcome of this filter. Here, we iterated the BEEPS 10 times with a Gaussian range filter, σ = 10, and the spatial decay λ = 0.1.

This plugin can find the smallest bounding box of an image (or a rectangular part defined by a selection) by cropping as much background as possible. Found in Fiji, under Image> Adjust.

In the version labeled with (guess background color), the plugin tries to determine the background color by looking at the pixels on the border of the image, while Auto Crop uses the currently selected background color which can be changed by double-clicking on the pipette symbol or using the Image > Color > Color Picker....

Instead of cropping right away, you can set the selection to the rectangle that would be cropped to using Edit > Selection > Select Bounding Box.

Fast Fourier Transform (FFT) for 2D/3D images.

Fiji Archipelago is a tool designed to make it easy for programmers to export Fiji/ImageJ functionality over a network to several other computers.

A canvas plugin using JFreeChart to show intensity profile of a specific row or column. Initially used in a 1-row image of 1D signal representation. Can also used with Micro-Manager for Icy Plugin to show 1D signal from hardware like data acquisition device as waveform. Common 2D+ sequence is also supported. Using it by select the plugin icon in the canvas type combobox of the sequence window, a JFreeChart line chart will show up. As an alternative plugin to Intensity Profile, this plugin is modified from "Intensity Profile" by fab, special thanks to him for giving me the idea to make such a plugin.

This plugin has two components:

• Elastic Montage
  • montaging mosaics from overlapping tiles where the tiles have non-linear relative deformation
• Elastic Stack Alignment
  • alignment of deformed section series from serially sectioned volumes

Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.

Manual angle measurements. 

No javadoc accessible, but can be downloaded from the webpage. 

This plugin provides an extended depth of field algorithm to obtain in focus microscopic images of 3D objects and organisms using different algorithms: Sobel, variance, real and complex wavelets.

Manually selecting line ROIs and align two images. 

Plugin to perform Delaunay Triangulation, or draw the Voronoi Diagram for a given point ROI.

This plugin comes with Fiji.

Colocalizer block.

Exports connected components data in XLS. Exports All, by T or by ROI

Library used by Micro-Manager for fast acquisition.

Anisotropic filters are a class of filter that reduces noise in an image while trying to preserve sharp edges

There are two implementations of Tschumperle/ R. Deriche filter ("anisotropic diffusion") for ImageJ Plugin

1. in the "imaging book" codes: see the javadoc here.

2. in Xlib

From the plugin inline help:

" Align RGB planes v1.7 by G.Landini Changes the alignment of the RGB planes independently.

Red Green and Blue checkboxes switch ON and OFF the planes and undo the alignment since last plane change. Note that when switching planes, the portion of the previously edited plane left outside the image frame is lost. Rotation, Width and Height changes are interpolated (so there is some loss of sharpness) and do not retain the image portions outside the image frame. You can use the Resize2Rotate macro to avoid losing any image data.

The Rotate, Width and Height sliders set integer values, but fractional values can also be typed in the entry boxes. Just make sure you press [RETURN] after the number is typed.

The Revert button works only with single images, not stacks.

Note: When using stacks, 2 buttons [< Prev] and [Next >] are added to the panel. Do not use the slide bar in the stack window, but use those buttons instead."

Some functions for PDE filtering.

"This ImageJ plugin (CGE) is a semi-automatic tool to detect and track moving cell, and to measure the fluorescent protein expression level. CGE extracts the trajectory of the cells by tracking their displacements, makes the delineation of cell nucleus or whole cell, and finally yields measurements of various features, like reporter protein expression level, cell displacement."

This is an icy package that encapsulates tools to design and implement parametric active contours. The package provides fast 2D and 3D filters for image preprocessing, and a framework to create and evolve snakes defined by a set of control points.

This plugin stabilizes jittery image stacks using the Lucas-Kanade algorithm. It supports both grayscale and color images.

See also this tweet

This plugin generates theoretical PSFs, assuming they arise only from diffraction.

This plugin permit to measure the signal spread of a molecule with respect to the cell area.

This plugin comes with Fiji

This plugin can be used to estimate nonlinear distortions induced by the image acquisition process[1] . It does not require special calibration samples, but needs sufficient overlapping image areas with preferably high contrast. For further information on how to best arrange calibration images please see the documentation.

a dynamic version of the Reslice command.

Bundled with Fiji.

An ImageJ plugin for manually tracking objects by mouse clicking. 

This plugin is bundled with Fiji. 

This plugins allows debleaching of time sequences of fluorescence images.

Bundled with Fiji. "Do all" is the great feature...