Tag: MATLAB

2D-EM – Matlab package of 2D-EM Clustering approach

2D-EM

:: DESCRIPTION

2D-EM is a clustering algorithm approach designed for small sample size and high-dimensional datasets. To employ information corresponding to data distribution and facilitate visualization, the sample is folded into its two-dimension (2D) matrix form (or feature matrix). The maximum likelihood estimate is then estimated using a modified expectation-maximization (EM) algorithm.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Matlab

:: DOWNLOAD

2D-EM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2017 Dec 28;18(Suppl 16):547. doi: 10.1186/s12859-017-1970-8.
2D-EM clustering approach for high-dimensional data through folding feature vectors.
Sharma A, Kamola PJ, Tsunoda T.

TACTICS 2.21 – MATLAB Platform For Customized Time-Lapse Microscopy Analysis

TACTICS 2.21

:: DESCRIPTION

TACTICS is a versatile MATLAB toolbox for High Content Analysis (HCA) of microscopy data. TATICS has been developed for image cytometry of non-adherent cells such as hematopoietic cells.

::DEVELOPER

TACTICS Team

:: SCREENSHOTS

TACTICS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MatLab

:: DOWNLOAD

 TACTICS

:: MORE INFORMATION

Citation

TACTICS, an interactive platform for customized high-content bioimaging analysis.
Shimoni R, Pham K, Yassin M, Gu M, Russell SM.
Bioinformatics. 2013 Mar 15;29(6):817-8.

SBMLToolbox 4.1.0 – SBML models toolbox for MATLAB users

SBMLToolbox 4.1.0

:: DESCRIPTION

SBMLToolbox is built on top of libSBML and provides a set of basic functions allowing SBML models to be used in MATLAB. SBMLToolbox provides functions for reading, writing, and validating SBML models; viewing model structures in a simple GUI; converting models into a symbolic form suitable for use with MATLAB’s Symbolic Math Toolbox; and simulate models using MATLAB’s ordinary differential equation solvers.

SBMLToolbox works by translating SBML models to/from a MATLAB structure calledMATLAB_SBML. It provides facilities for manipulating this and its substructures within MATLAB, as well as functions for saving and loading MATLAB_SBML structures to/from MATLAB data files.

::DEVELOPER

Sarah Keating

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

SBMLToolbox ; Manual

:: MORE INFORMATION

Citation:

Keating, S. M., Bornstein, B. J., Finney, A., and Hucka M. (2006) SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics, 22(10):1275–1277.

SBMLToolbox License

BVS – Matlab toolbox for Bayesian logistic and Probit Regression

BVS

:: DESCRIPTION

BVS is a MATLAB toolbox for binary Bayesian variable selection (logistic and probit regression) suitable for high-dimensional data, including block MCMC samplers and a parallel tempering algorithm to speed up the sampling process.

::DEVELOPER

Manuela Zucknick

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Matlab

:: DOWNLOAD

 BVS

:: MORE INFORMATION

mobility 0.1 – Genomic Fluidity Perl & MATLAB Scripts

mobility 0.1

:: DESCRIPTION

mobility is a collection of Perl scripts to calculate gene-level similarity among annotated genomes. The scripts can be executed from the command line and the only dependencies are BioPerl and NCBI BLAST. Separately, we include a MATLAB script to calculate fluidity and its variance directly from matrices of shared and total gene counts.

::DEVELOPER

WeitzGroup@GeorgiaTech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

mobility

:: MORE INFORMATION

Citation:

Kislyuk et al.
Genomic fluidity: an integrative view of gene diversity within microbial populations
BMC Genomics 12: 32 (2011).

BQJavaLib 0.1 – Java Library for Matlab to Direct Access to the Bisque DataBase System.

BQJavaLib 0.1

:: DESCRIPTION

BQJavaLib is a Java library for Matlab that allows direct access to the Bisque DataBase system.

::DEVELOPER

The Center for Bio-Image Informatics

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BQJavaLib

:: MORE INFORMATION

Browse source on-line

Segtrack – C++ & MatLab Library for Image Tracking & Segmentation

Segtrack

:: DESCRIPTION

Segtrack is a library of MATLAB functions useful for prepocessing, segmenting, tracking, postprocessing, and other tasks used for treating biological image data. See the html main_index file included in the dowload package for more details.

::DEVELOPER

Scientific Inference Systems Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

Segtrack

:: MORE INFORMATION

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

contact:
T.Bacarian
tbacaria@uci.edu

Sassign 2 – C++ & MatLab Library for Image Target Tracking

Sassign 2

:: DESCRIPTION

SASSIGN is a tracking software based on softassign matching algorithm. sassign is C++ and MATLAB package for tracking larger numbers of closely positioned cells (landmarks) with similar geometrical characteristics through timeseries of frames where some cells may divide into two daughter cells. Each frame may contains repositioned cells from the previous frame with some of them divided into two parts, and/or a few number of outliers e.g. cells appeared/disappeared from the boundaries of the frame or miscounted due to preprocessing errors. The C++ processing module is based on an advanced version of the softassign algorithm where simulated annealing is used to minimize a global target function over all possible parent-parent or parent-daughters associations of cells. The Matlab part of the package consists of wrapper routines for running the code and building hierarchical tree of the cells evolution

::DEVELOPER

Scientific Inference Systems Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

Sassign

:: MORE INFORMATION

Tracking Cell Signals in Fluorescent Images; Gor et. al. (CVPR2005)

CLSM Tools 20080903 – MATLAB Library for Nuclear Segmentation & Lineage Analysis

CLSM Tools 20080903

:: DESCRIPTION

CLSM Tools is a MATLAB library for nuclear segmentation and lineage analysis.

CLSM or LSCM (Confocal laser scanning microscopy) is a technique for obtaining high-resolution optical images with depth selectivity.

::DEVELOPER

Biological Network Modeling Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

CLSM Tools

:: MORE INFORMATION

CLSM Tools is available from the BNMC for the campus community.