Software

Software

 

thumb

 

Atlas

ATLAS is a spot detection method. The spots size is automatically selected and the detection threshold adapts to the local image dynamics. ATLAS relies on the Laplacian of Gaussian (LoG) filter, which both reduces noise and enhances spots. A multiscale representation of the image is built to automatically select the optimal LoG variance.

Image type: 2D
Language: C/C++
OS: Linux, Mac OSX
Try online: Allgo
Download: GitLab

More information

thumb

 

Backwarping

Warp sequence with parametric motion model (1995-2013) C/C++

More information

thumb

 

C-CRAFT

Vesicle segmentation and background estimation (2014) C/C++, Java

More information

thumb

 

Cryo-Seg

Segmentation of tomograms in cryo-electron microscopy (2010)

thumb

 

Flux estimation

Particle and intensity flux estimation (2015) C/C++

More information

thumb

 

GenLoc3D

3D high-precision gene localization algorithm in cell nuclei (2014-2015)     Java (ImageJ)

More information

thumb

 

GcoPS

3D Colocalization analysis (2017) Java

More information

thumb

 

HotSpotDetection

3D Robust detection of fluorescence accumulation over time in video-microscopy (2007-2008) C/C++

More information

thumb

 

HullkGround

3D Convex Hull for background subtraction (2008-2009) C/C++, Java

More information

thumb

 

KLTracker

Track vesicle and POI in image sequences (2012) C/C++

More information

thumb

 

Motion2D

Estimate 2D parametric motion model (2012)C/C++

More information

thumb

 

MS-Detect

Detecting moving objects in image sequences by background subtraction (2008/2011) C/C++

More information

thumb

 

ND-SAFIR

ND-SAFIR is a software for denoising n-dimentionnal images especially dedicated to microscopy image sequence analysis. It is able to deal with 2D, 3D, 2D+time, 3D+time images have one or more color channel. It is adapted to Gaussian and Poisson-Gaussian noise which are usually encountered in photonic imaging. Several papers describe the detail of the method used in ndsafir to recover noise free images.

Image type: 2D, 3D, 2D+time, 3D+time
Language: C/C++, Java, matlab
OS: Linux, Windows, Mac OSX
Try online: Allgo
Download: GitLab

More information

thumb

 

OpticalFlow

Optical flow (2012) C/C++

More information

thumb

 

OWF

Non-local means and optimal weights for noise removal (2017) Matlab  and C/C++

More information

thumb

 

PBED

Patch-Based Event Detection (2009) C/C++

thumb

 

QuantEv

Spatio-temporal distribution analysis (2017) C/C++, Java

More information

thumb

 

THOT

Classification of particle trajectories into three types of diffusions (2017) Matlab

More information

thumb

 

CPAnalysis

Change point detection along particle trajectories (2018) Matlab

More information

thumb

TubuleJ

Toolbox to process electron cryo-microscope images of vitrified microtubules (2009) Java (imageJ)

More information

Demonstrations

Online demonstration of several softwares are available at the Inria Allgo platform: https://allgo.inria.fr/

Comments are closed.