QuantiFly v2 – Automated Drosophila Egg Counting

QuantiFly v2

:: DESCRIPTION

QuantiFly  is a software package for automating egg counting in Drosophila genetics research.

::DEVELOPER

The Wolfson Imaging Centre

:: SCREENSHOTS

QuantiFly

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 QuantiFly

:: MORE INFORMATION

Citation

QuantiFly: Robust Trainable Software for Automated Drosophila Egg Counting.
Waithe D, Rennert P, Brostow G, Piper MD.
PLoS One. 2015 May 18;10(5):e0127659. doi: 10.1371/journal.pone.0127659.

GridMos 1.0 – Mosaicing tool (in MATLAB) to Improve Cell Counting

GridMos 1.0

:: DESCRIPTION

GridMos is an open-source software tool conceived to build an image mosaic of a hemocytometer’s grid.

::DEVELOPER

GridMos team

:: SCREENSHOTS

GridMos

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • MatLab

:: DOWNLOAD

 GridMos

:: MORE INFORMATION

Citation

Improving reliability of live/dead cell counting through automated image mosaicing.
Piccinini F, Tesei A, Paganelli G, Zoli W, Bevilacqua A.
Comput Methods Programs Biomed. 2014 Dec;117(3):448-63. doi: 10.1016/j.cmpb.2014.09.004

CellTracker 1.0.3 – Cell Migration Detection

CellTracker 1.0.3

:: DESCRIPTION

is an image processing software to perform automated, semi-automated, and manual cell migration detection.

::DEVELOPER

CellTracker team

:: SCREENSHOTS

CellTracker

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • MatLab

:: DOWNLOAD

 CellTracker

:: MORE INFORMATION

Citation

CellTracker (not only) for dummies.
Piccinini F, Kiss A, Horvath P.
Bioinformatics. 2015 Nov 20. pii: btv686.

SDA 1.0 beta – Statistical DIGE Analyzer

SDA 1.0 beta

:: DESCRIPTION

The SDA is a Java-application for the statistical analysis of data from 2-Dimensional Difference Gel Electrophoresis (DIGE).

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

sda

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 SDA

:: MORE INFORMATION

FOCAL – Cluster Analysis for Super-Resolved Microscopy

FOCAL

:: DESCRIPTION

FOCAL (Fast Optimized Cluster Algorithm for Localizations) is a rapid density based algorithm for detecting clusters in localization microscopy datasets. FOCAL is easily optimized to reduce artifacts that commonly degrade image reconstructions and minimize the detection of false or pseudo clusters.

::DEVELOPER

Milstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • MatLab

:: DOWNLOAD

 FOCAL

:: MORE INFORMATION

Citation

Fast Optimized Cluster Algorithm for Localizations (FOCAL): A Spatial Cluster Analysis for Super-Resolved Microscopy.
Mazouchi A, Milstein JN.
Bioinformatics. 2015 Nov 4. pii: btv630.

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.

YouScope 1.2 Beta – Open-source Microscope Control software

YouScope 1.2 Beta

:: DESCRIPTION

YouScope is a free, open-source microscope control software compatible with most present-day automized microscopes. YouScope allows to easily automatize complex microscopy protocols using an user-friendly graphical interface

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

YouScope

::REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 YouScope

:: MORE INFORMATION

Citation

Curr Protoc Mol Biol. 2012 Apr;Chapter 14:Unit 14.21.1-23. doi: 10.1002/0471142727.mb1421s98.
Use of YouScope to implement systematic microscopy protocols.
Lang M, Rudolf F, Stelling J.

FiloDetect – Detect & Quantify Filopodia in Single-cell Fluorescence Confocal Microscopy Images

FiloDetect

:: DESCRIPTION

FiloDetect is an image analysis program for detecting and quantifying filopodia in single-cell fluorescence confocal microscopy images.

::DEVELOPER

Perkins Lab at the OHRI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX /Windows
  •  MatLab

:: DOWNLOAD

 FiloDetect

:: MORE INFORMATION

Citation

S. Nilufar, A. A. Morrow, J. M. Lee, T. J. Perkins
FiloDetect: Automatic Detection of Filopodia from Fluorescence Microscopy Images
BMC Syst Biol. 2013 Jul 23;7:66. doi: 10.1186/1752-0509-7-66.

ThunderSTORM 1.3 – ImageJ plugin for PALM and STORM data analysis and super-resolution imaging

ThunderSTORM 1.3

:: DESCRIPTION

ThunderSTORM is an open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy.

::DEVELOPER

Institute of Cellular Biology and PathologyFirst Faculty of MedicineCharles University in Prague, Czech Republic.

:: SCREENSHOTS

ThunderSTORM

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 ThunderSTORM

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 25. pii: btu202. [Epub ahead of print]
ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging.
Ovesný M, Křížek P, Borkovec J, Svindrych Z, Hagen GM.

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.