Trakem2 lens distortion correction


Calculates and corrects for lens-distortion models including chromatic abberation from confocal stacks.



nctuTW is a "high-throughput computer method of reconstructing the neuronal structure of the fruit fly brain. The design philosophy of the proposed method differs from those of previous methods. We propose first to compute the 2D skeletons of a neuron in each slice of the image stack. The 3D neuronal structure is then constructed from the 2D skeletons. Biologists tend to use confocal microscopes for optimal images in a slice for human visualization; and images in two consecutive slices contain overlapped information. Consequently, a spherical object becomes oval in the image stack; that is, neurons in the image stack do not reflect the true shape of the neuron. This is the main reason we chose not to work directly on the 3D volume.

The proposed method comprises two steps. The first is the image processing step, which involves computing a set of voxels that is a superset of the 3D centerlines of the neuron. The shortest path graph algorithm then computes the centerlines. The proposed method was applied to process more than 16 000 neurons. By using a large amount of reconstructions, this study also demonstrated a result derived from the reconstructed data using the clustering technique." (Extracted from reference publication:

Illustrative image shows gold standard (top) and method results (bottom). 




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."




ORION: Online Reconstruction and functional Imaging Of Neurons: segmentation and tracing of neurons for reconstruction.

A project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function. The goal of this project is to develop a computational and experimental framework to allow real-time mapping of functional imaging data (e.g., spatio-temporal patterns of dendritic voltages or intracellularions) to neuronal structure, during the very limited duration of an acute experiment.


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



"we propose a novel automatic 3D neuron reconstruction algorithm, named Rivulet, which is based on the multi-stencils fast-marching and iterative back-tracking. The proposed Rivulet algorithm is capable of tracing discontinuous areas without being interrupted by densely distributed noises." 

This plugin can be used with default parameters or with user-defined parameters.

Example image obtained from Rivulet Wiki website (




"we present a new fully automated 3D reconstruction algorithm, called TReMAP, short for Tracing, Reverse Mapping and Assembling of 2D Projections. Instead of tracing a 3D image directly in the 3D space as seen in majority of the tracing methods, we first trace the 2D projection trees in 2Dplanes, followed by reverse-mapping the resulting 2D tracing results back into the 3D space as 3D curves; then we use a minimal spanning tree (MST) method to assemble all the 3D curves to generate the final 3D reconstruction. Because we simplify a 3D reconstruction problem into 2D, the computational costs are reduced dramatically." 

Suitable for high throughput neuron image analysis (image sizes >10GB). This plugin can be used with default parameters or user-defined parameters.


APP2 (All-path pruning 2)


"Results: We developed all-path-pruning 2.0 (APP2) for 3D neuron tracing. The most important idea is to prune an initial reconstruction tree of a neuron’s morphology using a long-segment-first hierarchical procedure instead of the original termini-first-search process in APP. To further enhance the robustness of APP2, we compute the distance transform of all image voxels directly for a gray-scale image, without the need to binarize the image before invoking the conventional dis- tance transform. We also design a fast-marching algorithm-based method to compute the initial reconstruction trees without pre-com- puting a large graph. Thismethod allows us to trace large images.We bench-tested APP2 on ~700 3D microscopic images and found that APP2 can generate more satisfactory results in most cases than sev- eral previous methods."

This method can be used with default parameters or user-defined parameters (Fully or semi-automated)


APP (All-path pruning)


"We have developed an automatic graph algorithm, called the all-path pruning (APP), to trace the 3D structure of a neuron. To avoid potential mis-tracing of some parts of a neuron, an APP first produces an initial over-reconstruction, by tracing the optimal geodesic shortest path from the seed location to every possible destination voxel/pixel location in the image. Since the initial reconstruction contains all the possible paths and thus could contain redundant structural components (SC), we simplify the entire reconstruction without compromising its connectedness by pruning the redundant structural elements, using a new maximal- covering minimal-redundant (MCMR) subgraph algorithm. We show that MCMR has a linear computational complexity and will converge. We examined the performance of our method using challenging 3D neuronal image datasets of model organisms (e.g. fruit fly)"

This plugin can be used with default parameters or user-defined parameters.


Object Tracking and Metadata Management


The goal of this workflow is to track cells captured in a time-lapse movie of a syncytial blastoderm stage Drosophila embryo and quantify their movement.

This example shows an example of object tracking. This pipeline analyzes a time-lapse experiment to identify the cells and track them from frame to frame, which is challenging since the cells are also moving. In addition, this pipeline also extracts metadata from the filename and uses groups the images by metadata in order to independently process several sequences of images and output the measurements of each.

Sample images

A portion of a time lapse movie of a syncytial blastoderm stage Drosophila embryo with a GFP-histone gene which renders chromatin fluorescent in live embryos. The movie shows nuclear divisions 10 through 13.

Victoria Foe made this movie on a Bio-Rad Radiance 2000 laser scanning confocal microscope using a 40X 1.3NA oil objective. The frames are 7 seconds apart and plays at 30 frames per second

GFP-histone transformed files provided by Rob Saint

V.Foe and G.Odell, . 26 July 2001

has function