A Component is an implementation of certain image processing / analysis algorithms.

Each component alone does not solve a Bioimage Analysis problem.

These problems can be addressed by combining such components into workflows.




The phase contrast microscopy segmentation toolbox (PHANTAST) is a collection of open-source algorithms and tools for the processing of phase contrast microscopy (PCM) images. It was developed at University College London's department of Biochemical Engineering and CoMPLEX.

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An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks

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Align slices in stack


Align_slices in stack utilized the template matching function cvMatch_Template to do slice registration(alignment) based on a selected landmark.
This function will try to find the landmark or the most similar image pattern in every slice and translate each slice so that the landmark pattern will be the same position throughout the whole stack. It could be used to fix the drift of a time-lapse image stacks.

Source code: link

Input data: image stack
output data: image stack

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It implements the template matching function from the OpenCV library. The java interface of OpenCV was done through the javacv library. It is quite similar as the existing template matching plugin but runs much faster and users could choose among six matching methods: 

1.Squared difference

2.Normalized squared difference


4.Normalized cross-correlation

5.Correlation coefficient

6.Normalized correlation coefficient

The detailed algorithms could be found here.

The cvMatch_Template will search a specific object (image pattern) over an image of interest by the user-specified method. 

CSBDeep, a toolbox for Content-aware Image Restoration (CARE) in Knime


Deep learning based restoration, with guidelines for training. See also the Fiji plugin.

CSBDeep, a toolbox for Content-aware Image Restoration (CARE) in Fiji


Deep learning for fluorescence image restoration (denoising, deconvolution). Requires training on your data set but the procedure is described.


Docker ParaViewWeb


This ParaViewWeb Docker container is used by the Galaxy Project.  Paraview is an VTK based visualization server, for 3D.

ParaViewWeb in Galaxy


HyphaTracker Workflow

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.




LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation

Download instruction:

There is no download but you can easily install this plugin via ImageJ update site. If you reallu need to download the jar file, access the file in the update site repository (Link)

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kymograph generation


Kymograph generation under ImageJ:

one simple solution, plot a line (ROI line) on the first frame, where you want to generate the kymograph.


Image  / Stacks  / Reslice

It will generate a new image were Y dimension is the time, and X the position on the line you have drawn.

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