Tag: Segmentation

ilastik 1.3.3 – the Interactive Learning and Segmentation Toolkit

ilastik 1.3.3

:: DESCRIPTION

ilastik is a simple, user-friendly tool for image classification and segmentation in up to three spatial and one spectral dimension. Using it requires no experience in image processing.

::DEVELOPER

ilastik team

:: SCREENSHOTS

ilastik

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 ilastik

:: MORE INFORMATION

Citation

ilastik: Interactive Learning and Segmentation Toolkit
C. Sommer, C. Straehle, U. K?the, and F.A. Hamprecht
8th IEEE International Symposium on Biomedical Imaging (ISBI 2011),

FASeg 2.0 – Forward Backward Fragment Assembling Segmentation

 

FASeg 2.0

:: DESCRIPTION

FASeg is an R package that performs forward-backward fragment assembling segmentation for array-CGH and SNP array data

::DEVELOPER

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

FASeg

:: MORE INFORMATION

Citation

A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array.
Yu T, Ye H, Sun W, Li KC, Chen Z, Jacobs S, Bailey DK, Wong DT, Zhou X.
BMC Bioinformatics. 2007 May 3;8:145.

YeastSpotter 2.1 – Yeast Segmentation Web Tool

YeastSpotter 2.1

:: DESCRIPTION

YeastSpotter is a web application for the segmentation of yeast microscopy images into single cells. YeastSpotter is user-friendly and generalizable, reducing the computational expertise required for this critical preprocessing step in many image analysis pipelines.

::DEVELOPER

Alan Moses’ Computational Biology Lab,University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

YeastSpotter

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Nov 1;35(21):4525-4527. doi: 10.1093/bioinformatics/btz402.
YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells.
Lu AX, Zarin T, Hsu IS, Moses AM

CalMaTe 0.12.1 – Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

CalMaTe 0.12.1

:: DESCRIPTION

CalMaTe is a multi-array post-processing method of allele-specific copy-number estimates (ASCNs).

::DEVELOPER

Henrik Bengtsson <henrikb at braju.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R

:: DOWNLOAD

 CalMaTe

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1793-4. doi: 10.1093/bioinformatics/bts248. Epub 2012 May 9.
CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.
Ortiz-Estevez M1, Aramburu A, Bengtsson H, Neuvial P, Rubio A.

Rseg 1.0 – an R package to Optimize Segmentation of SNP array data

Rseg 1.0

:: DESCRIPTION

Rseg allows the user to define sample-specific thresholds to call gains and losses in an interactive way. It also allows the user to correct for RMA induced normalization artifacts in case of imbalance between losses and gains.

::DEVELOPER

Lamy P (plamy@cs.au.dk), Wiuf C, Ørntoft TF, Andersen CL.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R package

:: DOWNLOAD

 Rseg

:: MORE INFORMATION

Citation

Rseg–an R package to optimize segmentation of SNP array data.
Lamy P, Wiuf C, Ørntoft TF, Andersen CL.
Bioinformatics. 2011 Feb 1;27(3):419-20.

AMASS – MSI Analysis by Semi-supervised Segmentation

AMASS

:: DESCRIPTION

AMASS is a series of tools written in C++ that allows you to segment your mass spectrometry imaging dataset into regions with similar molecular signatures. The software allows for user input at each step of the process and returns the regions as well as the associated molecular signatures. It is composed of two dynamic libraries and a series of executables using the libraries as a base.

::DEVELOPER

UCSD Department of Computer Science and Engineering

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python
  • TCL/TK

:: DOWNLOAD

 AMASS

:: MORE INFORMATION

Citation

Bruand J, Alexandrov T, Sistla S, Wisztorski M, Mériaux C, Becker M, Salzet M, Fournier I, Macagno E, Bafna V.
AMASS: Algorithm for MSI Analysis by Semi-supervised Segmentation.
J Proteome Res 10(10):4734-43

MPCBS 1.1.1 – Multi-platform segmentation for DNA copy number data

MPCBS 1.1.1

:: DESCRIPTION

MPCBS (Multi-Platform Circular Binary Segmentation) is a software which pools statistical evidence across platforms during segmentation, and does not require pre-standardization of different data sources. It involves a weighted sum of t-statistics, which arises naturally from the generalized log-likelihood ratio of a multi-platform model.

::DEVELOPER

Nancy R. Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R Package

:: DOWNLOAD

 MPCBS

:: MORE INFORMATION

Citation

Zhang, NR, Senbabaoglu, Y and Li, J, 2010,
Joint Estimation of DNA Copy Number from Multiple Platforms.
Bioinformatics, 26, 153-160.

GeSICA 1.0.2 – Genome Segmentation from Intra-Chromosomal Associations

GeSICA 1.0.2

:: DESCRIPTION

GeSICA is a two-step strategy of segmenting the human genome into detailed genomic organizational units. In the first step, GeSICA calculates Interaction Ratio of each genomic bin to dichotomize the human genome into two types of states. Only the functional-related regions are taken into account in the second step — Markov Cluster Algorithm (MCL). And a number of clusters are thus generated. Finally, three types of files are generated as the output of GeSICA: the Interaction-Ratio wiggle file, the segmentation bed file and the MCL genomic clusters file.

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 GeSICA

:: MORE INFORMATION

Citation

Liu L, Zhang Y, Feng J, Zheng N, Yin J, Zhang Y.
GeSICA: genome segmentation from intra-chromosomal associations.
BMC Genomics 2012; 13:164.

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

Exit mobile version