CRImage 1.30.0 – Tumour Image analysis

CRImage 1.30.0

:: DESCRIPTION

CRImage provides image analysis tools for segmentation, classification, and downstream analysis of tumour section images.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

  CRImage

:: MORE INFORMATION

Citation

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling
Y. Yuan, H. Failmezger, O.M. Rueda, H.R. Ali, S. Gräf, S-F. Chin, R.F. Schwarz, C Curtis, M.J. Dunning, H. Bardwell, N. Johnson, S. Doyle, G. Turashvili, E. Provenzano, S. Aparicio, C. Caldas, F. Markowetz
Science Translational Medicine, 4, 157ra142 (2012)

KymoRod 0.10.0 – Matlab Graphical Interface for the Study of Hypocotyl Growth

KymoRod 0.10.0

:: DESCRIPTION

KymoRod is a method for automated kinematic analysis of rod-shaped plant organs.

::DEVELOPER

IJPB Modeling and digital imaging lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 KymoRod

:: MORE INFORMATION

Citation

KymoRod: A method for automated kinematic analysis of rod-shaped plant organs.
Bastien R, Legland D, Martin M, Fregosi L, Peaucelle A, Douady S, Moulia B, Höfte H.
Plant J. 2016 Jun 29. doi: 10.1111/tpj.13255.

MorphoLibJ 1.2.2 – Collection of Mathematical Morphology Methods and Plugins for ImageJ

MorphoLibJ 1.2.2

:: DESCRIPTION

The MorphoLibJ library proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins.

::DEVELOPER

IJPB Modeling and digital imaging lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 MorphoLibJ

:: MORE INFORMATION

Citation

MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ.
Legland D, Arganda-Carreras I, Andrey P.
Bioinformatics. 2016 Jul 13. pii: btw413.

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.

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

3DEM Loupe – Normal Mode Analysis (NMA) of Electron Microscopy (EM) volumes

3DEM Loupe

:: DESCRIPTION

3DEM Loupe allows Normal Mode Analysis (NMA) of Electron Microscopy (EM) volumes . Results can be fully explored in 3D through animations and movies generated by the server, and special care has been given to a user-friendly interface

::DEVELOPER

Biocomputing Unit – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.
Nogales-Cadenas R, Jonic S, Tama F, Arteni AA, Tabas-Madrid D, Vázquez M, Pascual-Montano A, Sorzano CO.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W363-7. doi: 10.1093/nar/gkt385.

Scipion 1.0.0 – An Image Processing Framework for 3D Electron Microscopy

Scipion 1.0.0

:: DESCRIPTION

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers.

::DEVELOPER

Biocomputing Unit – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Xmipp

:: DOWNLOAD

  Scipion

:: MORE INFORMATION

Citation:

Scipion: a software framework toward integration, reproducibility and validation in 3D Electron Microscopy.
de la Rosa-Trevín JM, Quintana A, Del Cano L, Zaldívar A, Foche I, Gutiérrez J, Gómez-Blanco J, Burguet-Castell J, Cuenca-Alba J, Abrishami V, Vargas J, Otón J, Sharov G, Vilas JL, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano CO, Carazo JM.
J Struct Biol. 2016 Apr 20. pii: S1047-8477(16)30079-X. doi: 10.1016/j.jsb.2016.04.010

A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.
Sorzano CO, Vargas J, de la Rosa-Trevín JM, Otón J, álvarez-Cabrera AL, Abrishami V, Sesmero E, Marabini R, Carazo JM.
J Struct Biol. 2015 Mar;189(3):213-9. doi: 10.1016/j.jsb.2015.01.009.

OMERO 5.2.2 – Management & Analysis of Biological Microscope Images

OMERO 5.2.2

:: DESCRIPTION

OMERO is client-server Java software for visualisation, management and analysis of biological microscope images. The software consists of the OMERO server which can be accessed by a number of different clients. The OMERO clients allow the scientist to remotely manage, view, annotate and measure multi-dimensional images from anywhere. OMERO can also be extended to support data analysis.

::DEVELOPER

OME Development Teams

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • java

:: DOWNLOAD

OMERO server/Clients/ImageJ plugin

:: MORE INFORMATION

Citation

Metadata management for high content screening in OMERO.
Li S, Besson S, Blackburn C, Carroll M, Ferguson RK, Flynn H, Gillen K, Leigh R, Lindner D, Linkert M, Moore WJ, Ramalingam B, Rozbicki E, Rustici G, Tarkowska A, Walczysko P, Williams E, Allan C, Burel JM, Moore J, Swedlow JR.
Methods. 2015 Oct 22. pii: S1046-2023(15)30125-0. doi: 10.1016/j.ymeth.2015.10.006.

Nat Methods. 2012 Feb 28;9(3):245-53. doi: 10.1038/nmeth.1896.
OMERO: flexible, model-driven data management for experimental biology.
Allan C,et al.

ct3d 0.1 / at3d 0.1 – Cell Tracking Tools

ct3d 0.1 / at3d 0.1

:: DESCRIPTION

ct3d is a command-line tool for tracking cells in time series of 2D images or 3D image stacks. ct3d performs the basic cell tracking as a command line tool.

Visualization, exploration, and evalutation of the results can be done through the graphical user interface of at3d.

::DEVELOPER

Hang Xiao and Axel Mosig, THE RUB BIOINFORMATICS GROUP

:: SCREENSHOTS

at3d

:: REQUIREMENTS

:: DOWNLOAD

 ct3d / at3d

:: MORE INFORMATION

Citation

Ct3d: tracking microglia motility in 3D using a novel cosegmentation approach.
Xiao H, Li Y, Du J, Mosig A.
Bioinformatics. 2011 Feb 15;27(4):564-71. doi: 10.1093/bioinformatics/btq691. Epub 2010 Dec 24.

Cytomine 1.0 – Collaborative Analysis of Multi-gigapixel Images

Cytomine 1.0

:: DESCRIPTION

Cytomine is an open-source rich internet application for collaborative analysis of multi-gigapixel images

::DEVELOPER

Cytomine team

:: SCREENSHOTS

Cytomine

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 Cytomine

:: MORE INFORMATION

Citation:

Collaborative analysis of multi-gigapixel imaging data using Cytomine.
Marée R, Rollus L, Stévens B, Hoyoux R, Louppe G, Vandaele R, Begon JM, Kainz P, Geurts P, Wehenkel L.
Bioinformatics. 2016 Jan 10. pii: btw013.