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.


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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The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders.



A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O.

The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model).

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Globals for Images · SimFCS


Software for analysis, visualization, simulation, and acquisition  of data from spectroscopy and fluorescence microscopy.

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Measures wound-healing assay videos, 

 For each video, the velocity and the order parameter are analyzed in time and space to extract quantitative parameters characterizing the cell motility phenotype. The different conditions (videos) can then be classified according to these parameters.




WND-CHARM is a multi-purpose image classifier that can be applied to a wide variety of image classification tasks without modifications or fine-tuning, and yet provides classification accuracy comparable to state-of-the-art task-specific image classifiers. WND-CHARM can extract up to ~3,000 generic image descriptors (features) including polynomial decompositions, high contrast features, pixel statistics, and textures. These features are derived from the raw image, transforms of the image, and compound transforms of the image (transforms of transforms). The features are filtered and weighted depending on their effectiveness in discriminating between a set of predefined image classes (the training set). These features are then used to classify test images based on their similarity to the training classes. This classifier was tested on a wide variety of imaging problems including biological and medical image classification using several imaging modalities, face recognition, and other pattern recognition tasks. WND-CHARM is an acronym that stands for "Weighted Neighbor Distance using Compound Hierarchy of Algorithms Representing Morphology."

Generated features



SOAX is an open source software tool to extract the centerlines, junctions and filament lengths of biopolymer networks in 2D and 3D images. It facilitates quantitative, reproducible and objective analysis of the image data. The underlying method of SOAX uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then stretch along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments.

SOAX provides 3D visualization for exploring image data and visually checking results against the image. Quantitative analysis functions based on extracted networks are also implemented in SOAX, including spatial distribution, orientation, and curvature of filamentous structures. SOAX also provides interactive manual editing to further improve the extraction results, which can be saved in a file for archiving or further analysis. Useful for microtubules or actin filaments.

Observation: Depending on the operating system, the installation may or may not require Boost C++, ITK and VTK libraries. Windows has a standalone executable application without the need of those. 

snapshot microtubules soax



an open source ImageJ plugin suite for super-resolution structured illumination microscopy data quality control

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Simcheck screenschot

Angiogenesis Analyzer for ImageJ



The "Angiogenesis Analyzer" allows analysis of cellular networks. Typically, it can detect and analyze the pseudo vascular organization of endothelial cells cultured in gel medium

...a simple tool to quantify the ETFA (Endothelial Tube Formation Assay) experiment images by extracting characteristic information of the network.

The outputs are network feature parameters.

Sample images



Source code


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