AdipoCount – Automatic Adipocyte Counting

AdipoCount

:: DESCRIPTION

AdipoCount is an automatic adipoytes counting system using image processing algorithms, which can significantly imporve the efficency of adipoytes counting.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

AdipoCount

:: MORE INFORMATION

Citation:

Front Physiol. 2018 Feb 20;9:85. doi: 10.3389/fphys.2018.00085. eCollection 2018.
AdipoCount: A New Software for Automatic Adipocyte Counting
Xuhao Zhi, Jiqiu Wang, Peng Lu, Jue Jia, Hong-Bin Shen, Guang Ning

AnnoFly – Annotation of Drosophila Embryonic Images Based on an Attention-Enhanced RNN Model

AnnoFly

:: DESCRIPTION

AnnoFly is a new annotator for the fruit fly embryonic images.Driven by an attention-enhanced RNN model, it can weight images of different qualities, so as to focus on the most informative image patterns.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

AnnoFly 

:: MORE INFORMATION

Citation:

Bioinformatics. 2019 Aug 15;35(16):2834-2842. doi: 10.1093/bioinformatics/bty1064.
AnnoFly: Annotating Drosophila Embryonic Images Based on an Attention-Enhanced RNN Model
Yang Yang , Mingyu Zhou , Qingwei Fang , Hong-Bin Shen

TOMOJ 2.6 – Tools for Electron Tomography

TOMOJ 2.6

:: DESCRIPTION

TomoJ is a plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ.TomoJ provides a user-friendly interface for alignment, reconstruction, and combination of multiple tomographic volumes and includes the most recent algorithms for volume reconstructions used in three-dimensional electron microscopy (the algebraic reconstruction technique and simultaneous iterative reconstruction technique) as well as the commonly used approach of weighted back-projection.

::DEVELOPER

TOMOJ team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 TomoJ

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Aug 6;8:288.
TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy.
Messaoudi C, Boudier T, Sanchez Sorzano CO, Marco S.

Melanie 8.0 – 2D Gel Analysis Platform

Melanie 8.0

:: DESCRIPTION

Melanie provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE gels. The superior spot detection and matching algorithms facilitate the extraction of statistically valid differences between groups of 2-D gels, while requiring minimal user intervention and therefore speeding up analysis time.

::DEVELOPER

Geneva Bioinformatics (GeneBio) SA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Melanie

:: MORE INFORMATION

Make2D-DB II 3.10.2 – Gel Electrophoresis 2D-PAGE Databases

Make2D-DB II 3.10.2

:: DESCRIPTION

Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date two-dimensional gel electrophoresis (2D-PAGE) databases.  It converts data from various formats into a relational format. The tool offers the possibility to automatically update data related to numerous external data resources in a highly consistent manner. It is also possible with this tool to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point.

::DEVELOPER

The SIB Swiss Institute of Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Make2D-DB II 

:: MORE INFORMATION

Citation

Mostaguir K, Hoogland C, Binz PA, Appel RD.
The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases.
Proteomics. 2003 Aug;3(8):1441-4.

MSight 3.0.2 – Image Analysis for LCMS

MSight 3.0.2

:: DESCRIPTION

MSight was specifically developed for the representation of mass spectra along with data from the separation step. The software allows graphical exploration inside huge dataset and gives the scientist access to information that previously was hidden.

::DEVELOPER

Alan Bridge’s group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MSight

:: MORE INFORMATION

Citation

Patricia M. Palagi, Daniel Walther, Manfredo Quadroni, Sébastien Catherinet, Jennifer Burgess, Catherine G. Zimmermann-Ivol, Jean-Charles Sanchez, Pierre-Alain Binz1,, Denis F. Hochstrasser, Ron D. Appel
MSight: An image analysis software for liquid chromatography-mass spectrometry
Proteomics (2005; 5: 2381-2384)

MELANIE VIEWER 7.0.7 – Visualize Gels and Related Data obtained from Melanie

MELANIE VIEWER 7.0.7

:: DESCRIPTION

Melanie Viewer is made available free of charge to help researchers visualize gels and related data obtained through the use of the full version of Melanie by colleagues. It can also be used to view annotated gels from databases such as SWISS-2DPAGE, or any other image files with an appropriate format (.tif, .gel, …).

::DEVELOPER

The Proteome Informatics group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MELANIE VIEWER

:: MORE INFORMATION

HiTRACE 2.2.0 / HiTRACE-Web – High-Throughput Robust Analysis for Capillary Electrophoresis

HiTRACE 2.2.0 / HiTRACE-Web

:: DESCRIPTION

HiTRACE is a suite of robust and efficient analysis software to facilitate the analysis of large-scale high-throughput CE data.It has been intensively used for quantitating data for RNA and DNA based on the mutate-and-map methodology, chromatin footprinting, and other high-throughput structure mapping techniques.

HiTRACE-Web is an online version of HiTRACE that presents both standard features previously available only in the MATLAB environment as well as additional features such as automated band annotation and flexible adjustment of annotations, all via an integrative, user-friendly, and interactive environment.

::DEVELOPER

Das Lab , Seoul National University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX/ Windows
  • MatLab

:: DOWNLOAD

 HiTRACE

:: MORE INFORMATION

Citation

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis.
Kim H, Cordero P, Das R, Yoon S.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W492-8. doi: 10.1093/nar/gkt501.

HiTRACE: high-throughput robust analysis for capillary electrophoresis.
Yoon S, Kim J, Hum J, Kim H, Park S, Kladwang W, Das R.
Bioinformatics. 2011 Jul 1;27(13):1798-805. doi: 10.1093/bioinformatics/btr277

img2net – Automated Network-based Analysis of Imaged Phenotypes

img2net

:: DESCRIPTION

Img2net is a software to automatedly analyze such structures by reconstructing the underlying network, computing relevant network properties, and statistically comparing networks of different types or under different conditions.

::DEVELOPER

Systems biology and Mathematical Modelling

:: SCREENSHOTS

img2net

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Img2net

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 26. pii: btu503.
img2net: automated network-based analysis of imaged phenotypes.
Breuer D, Nikoloski Z.

IMOD 4.9.12 – Tomographic 3D Reconstruction & Modeling

IMOD 4.9.12

:: DESCRIPTION

IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.

::DEVELOPER

The Boulder Lab for 3D Electron Microscopy

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

IMOD ; source code

:: MORE INFORMATION

The citation is: Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116:71-76. For tomographic reconstruction, see also: Mastronarde, D. N. (1997) Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120:343-352.