SIMToolbox 1.2 – MATLAB toolbox for Structured Illumination Fluorescence Microscopy

SIMToolbox 1.2

:: DESCRIPTION

SIMToolbox is an open-source, modular set of functions for MATLAB designed for processing data acquired by structured illumination microscopy.

::DEVELOPER

Multimedia Technology Group

:: SCREENSHOTS

SIMToolbox

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 SIMToolbox

:: MORE INFORMATION

Citation

SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy.
Křížek P, Lukeš T, Ovesný M, Fliegel K, Hagen GM.
Bioinformatics. 2015 Oct 6. pii: btv576.

estrna – Estimation of Fluorescence-tagged RNA numbers from Spot Intensities

estrna

:: DESCRIPTION

estrna is a novel automated method for classifying pixel intensities of fluorescent spots to RNA numbers.

::DEVELOPER

by Hakkinen, Kandhavelu, Garasto, and Ribeiro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MATLAB

:: DOWNLOAD

 estrna

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 22. [Epub ahead of print]
Estimation of fluorescence-tagged RNA numbers from spot intensities.
Häkkinen A1, Kandhavelu M, Garasto S, Ribeiro AS.

AFDP v2.4a – Automated Fluorescence Data Processing

AFDP v2.4a

:: DESCRIPTION

AFDP is intended for processing and analysis of a series of fluorescence spectra recorded within a serial experiment like, for example, unfolding or titration series.

::DEVELOPER

Hofmann Laboratory, Eskitis Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 AFDP

 :: MORE INFORMATION

Citation

Hofmann, A., Wlodawer, A. (2002)
PCSB – a programme collection for structural biology and biophysical chemistry.
Bioinformatics 18, 209-210.

FISHtrees – Phylogenetic Analysis of Multiprobe Fluorescence in situ Hybridization data

FISHtrees

:: DESCRIPTION

FISHtrees” is a software program:
1) to parse copy numbers of multiple Fluorescence In Situ Hybridization (FISH) probe signals in a single-cell assay;
2) to analyze probe signals across multiple single-cell assays in a patient data file;
3) to model tumorigenesis as a tree of tumor progression paths for a given probe on a given patient data file;
4) to merge multiple tumorigenesis trees to represent multiple probes on a given patient data file;
5) to compute consensus multiple joint tumorigenesis trees representing multiple patient data files into a network as a graph of tumor progression pathways.

::DEVELOPER

FISHtrees team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FISHtrees

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i189-98. doi: 10.1093/bioinformatics/btt205.
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations.
Chowdhury SA1, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R.

WellReader 3.0 – Analysis of Fluorescence and Luminescence Reporter Gene data

WellReader 3.0

:: DESCRIPTION

WellReader implements computational methods developed for the analysis of the dynamics of gene expression in microorganisms, measured by means of fluorescent and luminescent reporter genes.

::DEVELOPER

the  Ibis group at  INRIA Grenoble-Rhône-Alpes.

:: SCREENSHOTS

WellReader

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Matlab 

:: DOWNLOAD

 WellReader

:: MORE INFORMATION

Citation

Bioinformatics. 2010 May 1;26(9):1262-3. doi: 10.1093/bioinformatics/btq016. Epub 2010 Jan 22.
WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.
Boyer F, Besson B, Baptist G, Izard J, Pinel C, Ropers D, Geiselmann J, de Jong H.

Visual3D 1.2 – Generate 3D Visualization of Fluorescence Microscopy Images

Visual3D 1.2

:: DESCRIPTION

Visual3D uses OpenGL textures to generate a 3D visualization of confocal and wide field fluorescence microscopy images. Custom color palettes can be applied to grey value images. AVI movies can be created with a build in script engine.

::DEVELOPER

AMC, CMO, Amsterdam, The Netherlands – Contact: R.A.Hoebe -at- amc.nl

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Visual3D

:: MORE INFORMATION

This software is free to anyone, just for fun send author a postcard:
AMC, Cell biology & Histology CMO, Ron Hoebe, Room M3-106-1
Meibergdreef 15, 1105 AZ  Amsterdam, The Netherlands