FlyLimbTracker is  a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behaving Drosophila flies. This approach can be used to measure leg segment motions during a variety of locomotor and grooming behaviors.

For now the plugin have to be downlaoded directly from the EPFL website (see link), not from the search bar as usual in ICY.


Drosophila track legs



OpenCL (Open Computing Language) is a framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), field-programmable gate arrays (FPGAs) and other processors or hardware accelerators. OpenCL specifies programming languages (based on C99 and C++11) for programming these devices and application programming interfaces (APIs) to control the platform and execute programs on the compute devices. OpenCL provides a standard interface for parallel computing using task- and data-based parallelism.

OpenCL is an open standard maintained by the non-profit technology consortium Khronos Group. Conformant implementations are available from AlteraAMDAppleARMCreativeIBMImaginationIntelNvidiaQualcommSamsungVivanteXilinx, and ZiiLABS.[7][8]


ATLAS Vesicle segmentation method


Part of ATLAS software

Comment / Instructions: 

You can upload your image at the Mobyle@SERPICO portal and download the result. The workflow is only available online, i.e. no download possible.



By combining multiple image alignment and tracing into one program, Reconstruct (TM) allows images to be processed more efficiently. Tracing can be done directly on the transformed images and alignments can be asily modified. Reconstruct (TM) was developed from years of experience working with high magnification serial section images of brain tissue. (Extracted from User Manual)

"The original platform of the Reconstruct program allows a user to trace objects in serial sections by manually drawing the outline of each object on each section, which is time-consuming. We modified Reconstruct to enable semi-automatic tracing of axons using a region-growing algorithm called wildfire."


Adipocyte quantification MATLAB


Analysis of adipocyte number and size. The original code and example images supposed to be discovered at but currently the webpage is missing the code and sample images.

has topic
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Neural Circuit Tracer


Neural Circuit Tracer (NCTracer) is open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer has more than one workflow available for neuron tracing. 

"The Neural Circuit Tracer is open source software built using Java (Sun Microsystems) and Matlab (MathWorks, Inc., Natick MA). It is based on the core of ImageJ ( and the graphic user interface has been developed by using Java Swings. The software combines anumber of functionalities of ImageJ with several newly developed functions for automated and manual tracing of neurites. The Neural Circuit Tracer is designed in a way
that will allow the users to add any plug-ins developed for ImageJ. More importantly, functions written in MatLab and converted into Java with Matlab JA toolbox can also be added to the Neural Circuit Tracer." 

Example of output from Neural Circuit Tracer



Spotsizer is a software tool that automates analysis of large volumes of photographic images of growing microbes.

screenshot of the spotsizer gui


Free-D is a three-dimensional (3D) reconstruction and modeling software. It allows to generate, process and analyze 3D point and surface models from stacks of 2D images. Free-D is an integrated software, offering in a single graphical user interface all the functionalities required for 3D modeling. It runs on Linux, Windows, and MacOS. Free-D is developed by the Modeling and Digital Imaging team of the Institut Jean-Pierre Bourgin, INRA Versailles, France.
need a thumbnail

Focal Adhesion Analysis Server


The website implements a set of computer vision algorithms designed to automatically process time-lapse images of fluorescently labeled focal adhesion proteins in motile cells. The methods associated with the processing have been published in PLOS One and Cell.

The publication describes a quantitative analysis of focal adhesion dynamics that have been imaged using TIRF. All image processing steps are well explained or referenced.

To better understand the dynamic regulation of focal adhesions, we have developed an analysis system for the automated detection, tracking, and data extraction of these structures in living cells. This analysis system was used to quantify the dynamics of fluorescently tagged Paxillin and FAK in NIH 3T3 fibroblasts followed via Total Internal Reflection Fluorescence Microscopy (TIRF). High content time series included the size, shape, intensity, and position of every adhesion present in a living cell. These properties were followed over time, revealing adhesion lifetime and turnover rates, and segregation of properties into distinct zones.

has function



Neuron studio is a software package to reconstruct neurons from 3D confocal images. Reconstruction can be done manually, semi-manually or fully automatic. The images as well as the detected objects are rendered in 3D. A spine detection and classification function is also included. Results can be exported as a text file with coords of the spines. It seems that active development has stopped in 2009. NeuronStudio is being developed at the Computational Neurobiology and Imaging Center (CNIC), a research laboratory at the Neuroscience Department of the Mount Sinai School of Medicine in New York.

NeuronStudio can be used with default parameters or user-defined parameters (Fully or semi-automated).