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)

Costanza 1.0 – ImageJ Plugin for Image Segmentation & Analyzing Stacks

Costanza 1.0

:: DESCRIPTION

Costanza (COnfocal STack ANalyZer Application) is a Image segmentation software developed for 3D confocal data. Implemented in Java as a plugin to ImageJ.

Costanza is used to segment compartments (cells) in a stack and to extract quantitative data for the extracted compartments, including intensities from a second stack.

::DEVELOPER

Michael Green, Pawel Krupinski, Pontus Melke, Patrik Sahlin, Henrik Jönsson
Computational Biology & Biological Physics, Lund University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Costanza ; userguide.pdf.

:: MORE INFORMATION

Source code is available upon request (henrik at thep.lu.se).

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.

SME 1.8 – Sigmoid Model Explorer

SME 1.8

:: DESCRIPTION

SME (Sigmoid Model Explorer) is a Graphical User Interface of the Sigmoid Project. It is a front end that provides access to the web services of the pathway databases and Cellerator, the module responsible for simulations. Some of SME’s features are:

  • Query and retrieval of Cellerator Models in Sigmoid Database via web service
  • Graphical view of Cellerator Models with customizable icons
  • Custom selection and editing of model parameters
  • Remote simulation of customized models in Cellerator via web service

::DEVELOPER

SME Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

SME

:: MORE INFORMATION

Register to become a SIGMOID user.

SBML Converters 20100413 – Conversions to & from SBML

SBML Converters 20100413

:: DESCRIPTION

SBML Converters are several converters which transfer SBML to BioPax 2 and 3, SBML to XPP and SBML to Octave, etc.

Converters list:

  • SBML to Octave  (GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.)
  • SBML to XPP (XPP-Aut is a numerical analysis software. It permits to solve differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.)
  • SBML to SciLab (SciLab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications.)
  • SBML to CellML & CellML to SBML (CellML is an open standard based on the XML markup language like SBML. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The main difference between CellML and SBML is that the former is based on modules while the latter is based on hierarchical components.)
  • SBML to BioPax (The main objective of the BioPAX initiative is to develop a data exchange format for biological pathways that is flexible, extensible, optionally encapsulated and compatible with other standards and can be widely adopted in a timely manner.)
  • SBML to Dot (GraphViz is an open source graph visualization software. The language used to encode the graphics processed by GraphViz is called DOT. Note that a “dot” file can be used with other graphical software.)
  • SBML to SVG (Scalable Vector Graphics (SVG) is a language for describing two-dimensional graphics and graphical applications in XML. It is an open standard created by the World Wide Web Consortium.)

SBML Converters also have an online version.

::DEVELOPER

Computational Systems Neurobiology Group, EBI

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SBML Converters

:: MORE INFORMATION

Please send any help requests or bug reports to : biomodels-net-support at lists.sourceforge.net

KEGG2SBML 1.5.0 – Convert KEGG Pathway Database to SBML

KEGG2SBML 1.5.0

:: DESCRIPTION

KEGG2SBML can convert KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway database files to SBML using the KEGG LIGAND database. KEGG2SBML’s capabilities are currently limited to converting only KEGG Metabolic Pathway files and not other types of KEGG files.

::DEVELOPER

Akiya Jouraku, Nobuyuki Ohta and Akira Funahashi , Dept. of Biosciences and Informatics at Keio University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

KEGG2SBML

:: MORE INFORMATION

Citations

  1. Converting KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004).
  2. Converting the KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    5th International Conference on Systems Biology (ICSB 2004), October, 2004.

KEGG2SBML License

MICE 1.4 – Mouse Information & Classification Entity

MICE 1.4

:: DESCRIPTION

MICE (Mouse Information and Classification Entity) is a program aimed at facilitating the monitoring of animals in their facility. It consists of a virtual facility in which scientists can perform all the tasks done in the real world (i.e., receiving animals, breeding, etc…). Each animal is recorded with all associated information (birth date, cage number, ID number, tail analysis number, parents, genetic status, genetic background and more), allowing for reliable tracking. Animals can be identified, grouped, sorted, moved…, according to any parameter of interest to the scientist, including associated comments. Crossings are automatically processed by the program, which determines the new genetic background, generation number, cage location and due date.

MICE reminds the user when births are expected, and entering the newborn animals only requires a few clicks (of the mouse!). The genealogy of each animal can be determined in two different ways, including a visual tree from which each ancestor’s information can be retrieved.

::DEVELOPER

P. Pognonec

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

MICE for Win ; for Mac

:: MORE INFORMATION

Citation:

MICE, a program to track and monitor animals in animal facilities. BMC Genetics 2001 Mar;2(1):4

Any comment and/or proposal concerning this application is welcome! Please contact P. Pognonec for additional information.

FCSM – Frozen Cell Stock Monitor

FCSM

:: DESCRIPTION

FCSM (Frozen Cell Stock Monitor) is a virtual nitrogen tank to monitor frozen cell stocks.

FCSM aimed at facilitating the monitoring of biological samples (cell lines, sera, etc) stored in liquid nitrogen containers. It consists of a virtual container in which scientists can “store” their samples and a program recording the location of each sample, cell characteristics, storage dates, names of the manipulators, and much more. Additional comments and a photograph can be associated with each vial, allowing for reliable tracking of samples. Vials can then be identified according to any parameter of interest to the scientist including associated comments. Once identified, the location of these vials is visually presented, simplifying their localization in the real container during retrieval. Thawing of vials is recorded by the program, together with the date and the name of the manipulator.

::DEVELOPER

P. Pognonec

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

FCSM for Win ; for Mac

:: MORE INFORMATION

Citation:

Virtual nitrogen tank to monitor frozen cell stocks. Biotechniques 2000 Jul;29(1):122-6

Any comment and/or proposal concerning this application is welcome! Please contactP. Pognonec for additional information.

SBML2SMW 1.0 – Extract Celldesigner Model to Semantic Mediawiki

SBML2SMW 1.0

:: DESCRIPTION

SBML2SMW allows extracting Celldesigner model information, storing this information to a Semantic Mediawiki server and context-sensitive restoring and integration of this information in a Celldesigner model. The application consists of two parts: The Celldesigner-plugin itself which directly communicates with the Celldesigner and so has access to the Celldesigner models and the Translationserver which receives the extracted information and translates it into Semantic Mediawiki syntax and stores it there.

::DEVELOPER

fluid Operations AG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

SBML2SMW

:: MORE INFORMATION

Code license GNU Lesser General Public License

SBML2SMW: bridging System Biology with semantic web technologies for biomedical knowledge acquisition and hypothesis elicitation
Tobias Mathäß, Peter Haase, Hiroaki Kitano, Luca Toldo. 2nd Workshop of Ontologies in Biomedicine and Life Sciences, OBML2010, Mannheim, Germany.