Category: Cytometry / Cell

CLOCCS 2.0.0 – Characterizing Loss of Cell Cycle Synchrony

CLOCCS 2.0.0

:: DESCRIPTION

CLOCCS is a novel and flexible mathematical model that describes the dynamics of population distributions resulting from synchrony loss over time. The model captures multiple sources of synchrony loss, including effects related to cell reproduction.

::DEVELOPER

Alex Hartemink

:: SCREENSHOTS

CLOCCS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

  CLOCCS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 1;27(13):i295-303. doi: 10.1093/bioinformatics/btr244.
A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments.
Mayhew MB, Robinson JW, Jung B, Haase SB, Hartemink AJ.

cellgraphs – Datastructure to Describe Cells in Tissue

cellgraphs

:: DESCRIPTION

Cellgraphs are a datastructure to describe cells in tissue.

::DEVELOPER

cellgraphs team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CellProfiler

:: DOWNLOAD

 cellgraphs

:: MORE INFORMATION

Citation

CD30 cell graphs of Hodgkin lymphoma are not scale-free – An image analysis approach.
Schäfer H, Schäfer T, Ackermann J, Dichter N, Döring C, Hartmann S, Hansmann ML, Koch I.
Bioinformatics. 2015 Sep 11. pii: btv542.

cell-motility 2.0 – Analysis of Cell Motility Paths over time

cell-motility 2.0

:: DESCRIPTION

The cell_motility software is an open source Java application under the GNU-GPL license that provides a clear and concise analysis workbench for large amounts of cell motion data. Apart from performing the necessary calculations, the software also visualizes the original motion paths as well as the results of the calculations to help the user interpret the data.

::DEVELOPER

Computational Omics and Systems Biology Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 cell-motility

:: MORE INFORMATION

Citation

Martens et al.
Cell Motility: a cross-platform, open source application for the study of cell motion paths.
BMC Bioinformatics (2006) vol. 7 pp 289

Vcellid 0.4 /CellID 1.4.6 / Rcell 1.1-8 – Microscope-Based Cytometry Cell-finding, Tracking & Analysis

Vcellid 0.4 /CellID 1.4.6 / Rcell 1.1-8

:: DESCRIPTION

Cell-ID is an open-source cell-finding, tracking, and analysis package using microscope based cytometry. Cell-ID have been used  to track cells through time courses of cells containing fluorescent reporters, reporters of fluorescence translocation , and FRET reporters.

Vcellid is a graphic user interface for the Cell-ID software developed by Andrew Gordon. It was originally designed to provide a rapid visual feedback of the effects of different segmentation parameter values, and to ease the analysis of cell-tracking time course experiments.

Rcell is an R package for data analysis of Cell-ID output.

::DEVELOPER

Laboratorio de Biologia Molecular de Sistemas

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

Vcellid/CellID/ Rcell

:: MORE INFORMATION

References:

Gordon A, Colman-Lerner A, Chin TE, Benjamin KR, Yu, R.C., Brent R: (2007) Single-cell quantification of molecules and rates using open-source microscope-based cytometry. Nat Methods.

Chernomoretz, A., Bush, A.,Yu, R.,Gordon, A., and Colman-Lerner, A., [2008] Using Cell-ID1.4 with R for microscope-based cytometry. Current Protocols In Molecular Biology.

ParticleStats 0.3 – Analysis of Particle Motility and Cytoskeletal Polarity

ParticleStats 0.3

:: DESCRIPTION

ParticleStats is a web server and open source programs, which input the X,Y coordinate positions of objects in time, and output novel analyses, graphical plots and statistics for motile objects. ParticleStats comprises three separate analysis programs. First, ParticleStats:Directionality for the global analysis of polarity, for example microtubule plus end growth in Drosophila oocytes. Second, ParticleStats:Compare for the analysis of saltatory movement in terms of runs and pauses. This can be applied to chromosome segregation and molecular motor-based movements. Thirdly ParticleStats:Kymographs for the analysis of kymograph images, for example as applied to separation of chromosomes in mitosis.

::DEVELOPER

Russell S. Hamilton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • C Compiler / Python/ Perl

:: DOWNLOAD

 ParticleStats

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W641-6. doi: 10.1093/nar/gkq542. Epub 2010 Jun 11.
ParticleStats: open source software for the analysis of particle motility and cytoskeletal polarity.
Hamilton RS, Parton RM, Oliveira RA, Vendra G, Ball G, Nasmyth K, Davis I.

Cyflogic 1.2.1 – Flow Cytometry Data Analysis Tool

Cyflogic 1.2.1

:: DESCRIPTION

Cyflogic is a flow cytometry data analysis tool for Microsoft Windows enviroment. It has all “regular” analysis capabilities, such as dot plot, histogram and statistics. In addition, Cyflogic offers new innovative tools for your data analysis.

::DEVELOPER

CyFlo Ltd.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Cyflogic

:: MORE INFORMATION

Ferdinand 3.10 – Read and analyze FCS 3.0 data files collected by Flow Cytometers

Ferdinand 3.10

:: DESCRIPTION

Ferdinand is a freeware stand-alone program that reads FCS 3.0 data files and analyzes them from the distributions of fluorescent events. Ferdinand performs a number of analytical tasks when analyzing data collected by Flow Cytometers, machines which measure the optical and fluorescence properties of particles as they pass through lasers.

::DEVELOPER

Lawrence’s Lab

:: SCREENSHOTS

Ferdinand

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Ferdinand

:: MORE INFORMATION

ACME – Automated Cell Morphology Extraction

ACME

:: DESCRIPTION

ACME is a state-of-the-art open-source C++ software for reconstructing membranes to achieve high-quality whole cell segmentations. The software enables the quantification of cell morphologies, cell size, tissue interfaces, arrangement in tightly-packed tissues, and tissue geometry from time-lapse image sequences. The software is generic, modular, scalable to large datasets, and provides an easy API for interfacing with other software systems.

::DEVELOPER

the Megason Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX /Linux

:: DOWNLOAD

 ACME

:: MORE INFORMATION

Citation

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes.
Mosaliganti KR, Noche RR, Xiong F, Swinburne IA, Megason SG.
PLoS Comput Biol. 2012 Dec;8(12):e1002780. doi: 10.1371/journal.pcbi.1002780. Epub 2012 Dec 6.

CellAtlas 1.5 – Blood Cell Morphology Guide for Mobile

CellAtlas 1.5

:: DESCRIPTION

CellAtlas contains mini lectures written by hematology experts complemented by an extensive cell image database. The App also includes a game, CellQuiz. A fun and efficient way to test your knowledge in cell morphology.

::DEVELOPER

CellaVision

:: SCREENSHOTS

CellAtlas

:: REQUIREMENTS

  • Android / iPad /iPhone

:: DOWNLOAD

 CellAtlas for iOS / for Android

:: MORE INFORMATION