CONSERTING – Copy Number Segmentation by Regression Tree in Next Generation Sequencing

CONSERTING

:: DESCRIPTION

CONSERTING (Copy Number Segmentation by Regression Tree in Next Generation Sequencing) is an accurate method for detecting somatic DNA copy number variation in whole genome sequencing data.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R package

:: DOWNLOAD

 CONSERTING

:: MORE INFORMATION

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.

LEVER – Stem Cell Segmentation, Tracking and Lineaging

LEVER

:: DESCRIPTION

LEVER (Lineage Editing and Validation) is a collection of software tools for analyzing the development of proliferating (dividing) cells in time-lapse microscopy image sequences. LEVER includes algorithms for segmentation, tracking and lineaging. LEVER also includes a user interface that allows the segmentation, tracking and lineaging results to be validated, with any errors in the automated processing easily identified and quickly corrected

CloneView is an incredibly useful tool for visualizing the results from the LEVER program together with the image data.

::DEVELOPER

computational image sequence analysis

:: SCREENSHOTS

LEVER

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 LEVER

:: MORE INFORMATION

Citation

LEVER: software tools for segmentation, tracking and lineaging of proliferating cells.
Winter M, Mankowski W, Wait E, Temple S, Cohen AR.
Bioinformatics. 2016 Jul 16. pii: btw406.

copynumber 1.12.0 – Segmentation of Single- and multi-track Copy Number data by penalized least Squares Regression

copynumber 1.12.0

:: DESCRIPTION
The R package copynumber is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.

::DEVELOPER

Research Group for Biomedical Informatics (BMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R / BioCOnductor

:: DOWNLOAD

 copynumber

:: MORE INFORMATION

Citation:

BMC Genomics. 2012 Nov 4;13:591. doi: 10.1186/1471-2164-13-591.
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.
Nilsen G1, Liestøl K, Van Loo P, Moen Vollan HK, Eide MB, Rueda OM, Chin SF, Russell R, Baumbusch LO, Caldas C, Børresen-Dale AL, Lingjaerde OC.

Imaris 8.3 – Analysis, Segmentation and Interpretation of 3D and 4D Microscopy datasets

Imaris 8.3

:: DESCRIPTION

Imaris is Bitplane’s core scientific software module for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.

::DEVELOPER

BITPLANE AG

:: SCREENSHOTS

Imaris

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 Imaris

:: MORE INFORMATION

CellX 1.12 – MATLAB Image Segmentation Package

CellX 1.12

:: DESCRIPTION

CellX is a tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images.

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

 CellX

:: MORE INFORMATION

Citation

Using CellX to quantify intracellular events.
Mayer C, Dimopoulos S, Rudolf F, Stelling J.
Curr Protoc Mol Biol. 2013;Chapter 14:Unit 14.22.. doi: 10.1002/0471142727.mb1422s101.

Bioinformatics. 2014 Sep 15;30(18):2644-51. doi: 10.1093/bioinformatics/btu302. Epub 2014 May 21.
Accurate cell segmentation in microscopy images using membrane patterns.
Dimopoulos S, Mayer CE, Rudolf F, Stelling J.

snapCGH 1.38.0 – Segmentation, Normalisation And Processing of Array CGH data

snapCGH 1.38.0

:: DESCRIPTION

snapCGH is a softwaer for the analysis of array CGH data. It has been written to be compatible with limma so that the user can apply all of the preprocessing functions available within limma to array CGH data.

::DEVELOPER

Computational Biology Group, Department of Oncology, University of Cambridge

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 snapCGH

:: MORE INFORMATION

ilastik 1.1.5 – the Interactive Learning and Segmentation Toolkit

ilastik 1.1.5

:: 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),

sephaCe v3 – Segmentation of Adherent Biological Cell Boundaries

sephaCe v3

:: DESCRIPTION

sephaCe ( stands for “see phase of cells”,) is an open-source tool for automatic segmentation of adherent biological cell boundaries from brightfield microscopy images.

::DEVELOPER

Rehan Ali

:: SCREENSHOTS

sephaCe

:: REQUIREMENTS

  • Windows / MacOSX /Linux
  • Matlab

:: DOWNLOAD

 sephaCe

:: MORE INFORMATION