Category: Cytometry / Cell

CellOrganizer 2.8.1 – Image-derived Models of Subcellular Organization and Protein Distribution

CellOrganizer 2.8.1

:: DESCRIPTION

The CellOrganizer project provides tools for :learning generative models of cell organization directly from images/ storing and retrieving those models in XML files/ synthesizing cell images (or other representations) from one or more models

::DEVELOPER

CellOrganizer TEam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac /  Linux
  • MatLab

:: DOWNLOAD

  CellOrganizer

:: MORE INFORMATION

Citation

Methods Cell Biol. 2012;110:179-93.
CellOrganizer: Image-derived models of subcellular organization and protein distribution.
Murphy RF.

BayesFlow 0.1 – Latent Modeling of Flow Cytometry Cell Populations

BayesFlow 0.1

:: DESCRIPTION

BayesFlow is a Bayesian hierarchical model, that models the variation across indivuals for clow cytometry data.

::DEVELOPER

Jonas Wallin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 BayesFlow

:: MORE INFORMATION

Citation

Erratum to: BayesFlow: latent modeling of flow cytometry cell populations.
Johnsson K, Wallin J, Fontes M.
BMC Bioinformatics. 2016 Mar 31;17(1):149.

flowFit 1.24.0 – Estimate Proliferation in Cell-tracking Dye Studies

flowFit 1.24.0

:: DESCRIPTION

flowFit is a Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments.

::DEVELOPER

flowFit team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 flowFit

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 2.
flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies.
Rambaldi D1, Pece S, Di Fiore PP.

CellFinder 1.5.1 – Study Annotations, Bibliography, Gene and Protein Expression in Stem Cells and Derivatives

CellFinder 1.5.1

:: DESCRIPTION

CellFinder maps validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Jan;42(Database issue):D950-8. doi: 10.1093/nar/gkt1264. Epub 2013 Dec 3.
CellFinder: a cell data repository.
Stachelscheid H1, Seltmann S, Lekschas F, Fontaine JF, Mah N, Neves M, Andrade-Navarro MA, Leser U, Kurtz A.

TIMER – Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells

TIMER

:: DESCRIPTION

TIMER (Tumor IMmune Estimation Resource) is a comprehensive resource for the clinical relevance of tumor-immune infiltrates, including B cells, CD4 and CD8 T cells, neutrophils, macrophages and dendritic cells.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Cancer Res. 2017 Nov 1;77(21):e108-e110. doi: 10.1158/0008-5472.CAN-17-0307.
TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells.
Li T, Fan J, Wang B, Traugh N, Chen Q, Liu JS, Li B, Liu XS.

VirtualCytometry – Webserver for the Study of Immune Cell Differentiation using single-cell RNA sequencing data

VirtualCytometry

:: DESCRIPTION

VirtualCytometry is a webserver that provides computational platform for the study of immune cell differentiation using scRNA-seq data by enabling identification and validation of genes involved in immune cell differentiations via ‘Discovery Module’ and ‘Hypothesis Test Module’ respectively.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Aug 2. pii: btz610. doi: 10.1093/bioinformatics/btz610.
VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data.
Kim K, Yang S, Ha SJ, Lee I.

QSpec 1.0 / QSpec-Simu 1.0 – A Raman Spectrum Acquisition and Analysis System for Single-Cell

QSpec 1.0 / QSpec-Simu 1.0

:: DESCRIPTION

QSpec is an open-source framework of microorganism single-cell experimental platform that could support the full cycle of single-cell phenotyping: instrument control (including RACS platform control and microfluidic device control), single-cell image analysis, single-cell Raman profiling, single-cell profile comparison, etc.

QSpec-Simu is an open-source framework of virtual microorganism single-cell experimental platform

::DEVELOPER

Bioinformatics Group , Single-cell Reseearch Center of Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS).

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

QSpec / QSpec-Simu

:: MORE INFORMATION

Citation

Lihui R.; Xiaoquan S.; Yun W.; Jian X.; Kang N.,
QSpec: online control and data analysis system for single-cell Raman spectroscopy.
PeerJ. 2014 Jun 26;2:e436. doi: 10.7717/peerj.436. eCollection 2014.

CellMontage 2 – Gene Expression databases searching system for Cells-type Analysis

CellMontage 2

:: DESCRIPTION

CellMontage is a system for searching gene expression databases for similar cells or tissues to the query gene expression profile.

::DEVELOPER

Computational Biology Research Center[CBRC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Nov 15;23(22):3103-4. Epub 2007 Sep 25.
CellMontage: similar expression profile search server.
Fujibuchi W, Kiseleva L, Taniguchi T, Harada H, Horton P.

CoD – Inferring Immune-Cell Quantities Related to Disease States

CoD

:: DESCRIPTION

CoD (Cell-type of Disease) is a classification-based approach that relies on computational immune-cell decomposition in gene-expression datasets.

::DEVELOPER

Irit Gat-Viks laboratory.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linuc

:: DOWNLOAD

CoD

:: MORE INFORMATION

Citation:

CoD: inferring immune-cell quantities related to disease states.
Frishberg A, Steuerman Y, Gat-Viks I.
Bioinformatics. 2015 Aug 26. pii: btv498.

Schnitzcells – Quantitative Analysis of Fluorescent Time-lapse movies of Living Cells

Schnitzcells

:: DESCRIPTION

Schnitzcells is a MATLAB based software that allows for quantitative analysis of fluorescent time-lapse movies of living cells.  The software package is developed most specifically for bacteria and has been instrumental in analyzing  E.coli and B. subtilis movies.

::DEVELOPER

The Elowitz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MabLab

:: DOWNLOAD

 Schnitzcells

:: MORE INFORMATION

Citation

Young, J. W. ,Locke, J.C.W.,Altinok,A.,Rosenfeld,N.,Bacarian,T.,Swain,P.S.,Mjolsness,E.,Alon,U.,Elowitz,M.B.
Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy.
Nature Protocols 7, 80–88 (2012)