TimeLapseAnalyzer 1.34 – High Throughput data processing for Live Cell Imaging

TimeLapseAnalyzer 1.34

:: DESCRIPTION

Time Lapse Analyser (TLA) is a free, cross-platform, open source software for high throughput time-lapse data processing for live cell imaging.

::DEVELOPER

TimeLapseAnalyzer team

:: SCREENSHOTS

TimeLapseAnalyzer

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • MatLab
:: DOWNLOAD

 TimeLapseAnalyzer

:: MORE INFORMATION

Citation

Comput Methods Programs Biomed. 2011 Nov;104(2):227-34. doi: 10.1016/j.cmpb.2011.06.002. Epub 2011 Jun 25.
TimeLapseAnalyzer: multi-target analysis for live-cell imaging and time-lapse microscopy.
Huth J, Buchholz M, Kraus JM, M?lhave K, Gradinaru C, v Wichert G, Gress TM, Neumann H, Kestler HA.

SCIP 1.0 – Single-Cell Image Processor

SCIP 1.0

:: DESCRIPTION

SCIP is an open source multi-channel, multi-process, time-lapse morphological and functional microscopy images analyser.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

SCIP

:: MORE INFORMATION

Citation:

Martins L, Neeli-Venkata R, Oliveira SMD, Häkkinen A, Ribeiro AS, Fonseca JM.
SCIP: a single-cell image processor toolbox.
Bioinformatics. 2018 Dec 15;34(24):4318-4320. doi: 10.1093/bioinformatics/bty505. PMID: 29931314.

ZebIAT 1.0 – Zebrafish Image Analysis Tool

ZebIAT 1.0

:: DESCRIPTION

ZebIAT is a tool for registering zebrafish images acquired by fluorescence microscope as well as differential interference microscope. The tool offers automatic and semi-automatic methods to analyze images and thus allow, e.g. quantitative comparisons between images.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

 ZebIAT

 :: MORE INFORMATION

Citation:

T. Annila, E. Lihavainen, I.J. Marques, D.R. Williams, O. Yli-Harja and A.S. Ribeiro. 2013.
ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis.
BMC Bioinformatics 2013, 14(Suppl. 10):S5.

MAMLE 1.0 – Image Analysis of E. coli and other Bacteria

MAMLE 1.0

:: DESCRIPTION

MAMLE is a novel segmentation method for detecting cells within dense clusters. MAMLE executes cell segmentation in two main stages. The first relies on state of the art filtering technique, edge detection in multi resolution with morphological operator and threshold decomposition for adaptive thresholding. From this, a correction procedure is applied that exploits maximum likelihood estimate as an objective function. Also, it acquires morphological features from the initial segmentation for constructing the likelihood parameter, after which the final segmentation results are obtained.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

 CellSegment Tool

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013;14 Suppl 10:S8. doi: 10.1186/1471-2105-14-S10-S8. Epub 2013 Aug 12.
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE).
Chowdhury S, Kandhavelu M, Yli-Harja O, Ribeiro AS.

Mytoe – Image analysis of Mitochondria

Mytoe

:: DESCRIPTION

Mytoe is a software for analyzing mitochondrial dynamics from fluorescence microscope images. The program can be used for the analysis of spatial properties of the mitochondrial structure, as well as the motion of mitochondria.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

 Mytoe

 :: MORE INFORMATION

Citation:

Mytoe: automatic analysis of mitochondrial dynamics.
Lihavainen E, Mäkelä J, Spelbrink JN, Ribeiro AS.
Bioinformatics. 2012 Apr 1;28(7):1050-1. doi: 10.1093/bioinformatics/bts073.

CellAging – Study Segregation and Partitioning in Division in Cell Lineages of Escherichia coli

CellAging

:: DESCRIPTION

CellAging is a tool designed to automatically extract information on the segregation of aggregates to the cell poles and their partitioning in division and on cellular vitality from temporal images of E. coli cells, obtained by parallel brightfield and fluorescence microscopy.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MatLab

:: DOWNLOAD

 CellAging

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1708-9. doi: 10.1093/bioinformatics/btt194. Epub 2013 Apr 23.
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli.
Antti Hakkinen, Muthukrishnan AB, Mora A, Fonseca JM, Ribeiro AS.

MOSAIC 2016 – ImageJ plugin for Biological Fluorescence Microscopy

MOSAIC 2016

:: DESCRIPTION

MOSAIC (MOdels, Simulations, and Algorithms for Interdisciplinary Computing) , the image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy , are available as plugins for the popular free image processing software ImageJ.

::DEVELOPER

MOSAIC group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MOSAIC

:: MORE INFORMATION

Citation:

I. F. Sbalzarini and P. Koumoutsakos.
Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology,
Journal of Structural Biology 151(2):182-195, 2005.

HTML5 PivotViewer 1.0 – A HTML5 Data Exploration Tool for Image based data sets

HTML5 PivotViewer 1.0

:: DESCRIPTION

HTML5 PivotViewer is a novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image.

::DEVELOPER

The Computational Biology Research Group (CBRG)

:: SCREENSHOTS

PivotViewer

:: REQUIREMENTS

  • HTML5 Web Browser

:: DOWNLOAD

 HTML5 PivotViewer

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 21. pii: btu349. [Epub ahead of print]
HTML5 PivotViewer: High throughput visualisation and querying of image data on the web.
Taylor S1, Noble R2.

Bisque 0.5.8 – Platform for Bioimage Analysis & Management

Bisque 0.5.8

:: DESCRIPTION

Bisque (Bio-Image Semantic Query User Environment) was developed for the exchange and exploration of biological images. The Bisque system supports several areas useful for imaging researchers from image capture to image analsysis and querying. The bisque system is centered around a database of images and metadata. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content.

::DEVELOPER

The Center for Bio-Image Informatics

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Bisque

:: MORE INFORMATION

Citation:

Kristian Kvilekval, Dmitry Fedorov, Boguslaw Obara, Ambuj Singh and B.S. Manjunath,
Bisque: A Platform for Bioimage Analysis and Management
Bioinformatics, vol. 26, no. 4, pp. 544-552, Feb. 2010.

Scipion 3.0 – An Image Processing Framework for 3D Electron Microscopy

Scipion 3.0

:: 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

:: 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.