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.

SpotCaliper – Fast Wavelet-based Spot Detection with Accurate Size Estimation

SpotCaliper

:: DESCRIPTION

SpotCaliper is a novel wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size.

::DEVELOPER

Biomedical Imaging Group

:: SCREENSHOTS

SpotCaliper

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 SpotCaliper

:: MORE INFORMATION

Citation

SpotCaliper: Fast Wavelet-based Spot Detection with Accurate Size Estimation.
Püspöki Z, Sage D, Ward JP, Unser M.
Bioinformatics. 2015 Dec 10. pii: btv728.

ImgLib2 2.4.1 – Image Processing JAVA Library

ImgLib2 2.4.1

:: DESCRIPTION

ImgLib2 is a general-purpose, multidimensional image processing library.

::DEVELOPER

ImgLib2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

  ImgLib2

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):3009-11. doi: 10.1093/bioinformatics/bts543. Epub 2012 Sep 8.
ImgLib2–generic image processing in Java.
Pietzsch T, Preibisch S, Tomancák P, Saalfeld S.

OpenSPIM 20150427 – Open-access Light-sheet Microscopy Platform

OpenSPIM 20150427

:: DESCRIPTION

OpenSPIM is an Open Access platform for applying and enhancing Selective Plane Illumination Microscopy (SPIM).

::DEVELOPER

OpenSPIM team

:: SCREENSHOTS

OpenSPIM

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 OpenSPIM

:: MORE INFORMATION

Citation

Nat Methods. 2013 Jul;10(7):598-9. doi: 10.1038/nmeth.2507. Epub 2013 Jun 9.
OpenSPIM: an open-access light-sheet microscopy platform.
Pitrone PG, Schindelin J, Stuyvenberg L, Preibisch S, Weber M, Eliceiri KW, Huisken J, Tomancak P.

Fiji 20141125 – Image Processing Package based on ImageJ

Fiji 20141125

:: DESCRIPTION

Fiji (Fiji is Just ImageJ) is an image processing package. It can be described as a distribution of ImageJ together with Java, Java 3D and a lot of plugins organized into a coherent menu structure.

::DEVELOPER

Fiji Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Fiji

:: MORE INFORMATION

Publications introducing Fiji

PCaAnalyser – 2D-Image Analysis Based Module for Effective Determination of Prostate Cancer Progression in 3D Culture

PCaAnalyser

:: DESCRIPTION

PCaAnalyser uses novel algorithms that allow accurate and rapid quantitation of protein expression in 3D cell culture.

::DEVELOPER

Hoque’s Lab, University of New Orleans

:: SCREENSHOTS

PCaAnalyser

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 PCaAnalyser

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 20;8(11):e79865. doi: 10.1371/journal.pone.0079865. eCollection 2013.
PCaAnalyser: a 2D-image analysis based module for effective determination of prostate cancer progression in 3D culture.
Hoque MT1, Windus LC, Lovitt CJ, Avery VM.

AISO 0.3 – Image Segmentation tool

AISO 0.3

:: DESCRIPTION

AISO (Annotation of Image Segments with Ontologies) is an interactive image segmentation tool designed to allow curators of biological specimens to segment and annotate image data with ontology terms.

::DEVELOPER

The Jaiswal Lab

:: SCREENSHOTS

aiso

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Java

:: DOWNLOAD

 AISO

:: MORE INFORMATION

Citation

AISO: Annotation of Image Segments with Ontologies.
Lingutla NT, Preece J, Todorovic S, Cooper L, Moore L, Jaiswal P.
J Biomed Semantics. 2014 Dec 17;5(1):50. doi: 10.1186/2041-1480-5-50.

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