Cytometry Part A

Cover image for Vol. 87 Issue 9

Edited By: Attila Tárnok

Impact Factor: 2.928

ISI Journal Citation Reports © Ranking: 2014: 28/79 (BIOCHEMICAL RESEARCH METHODS); 109/184 (Cell Biology)

Online ISSN: 1552-4930

Associated Title(s): Cytometry Part B: Clinical Cytometry

All Virtual Issues

Virtual Issue: Microscopy in Cytometry: Innovative Microscopy

Virtual Issue: Microscopy in Cytometry: Microscopy and High-Throughput Microscopy

Virtual Issue: Microscopy in Cytometry: Image Cytometry

Virtual Issue: What cytometrists really like to read

Joint Virtual Issue on Stem Cells from Cytometry Part A, Cytometry Part B: Clinical Cytometry, Journal of Biophotonics, and Cell Proliferation

Virtual Issue: Microscopy in Cytometry: Innovative Microscopy



Using Surface Plasmon Resonance Imaging to Probe Dynamic Interactions Between Cells and Extracellular Matrix

Peterson, Alexander W.; Halter, Michael; Tona, Alessandro; Bhadriraju, Kiran; Plant, Anne L.

2010. 77A(9):895-903


Controlled Light Exposure Microscopy Reveals Dynamic Telomere Microterritories Throughout the Cell Cycle

De Vos, Winnok H.; Hoebe, R. A.; Joss, G. H.; Haffinans, W.; Baatout, S.; Van Oostveldt, P.; Manders, E. M. M.

2009. 75A(5):428-439


Insight into the Microbial Multicellular Lifestyle via Flow-Cell Technology and Confocal Microscopy

Pamp, Sunje Johanna; Sternberg, Claus; Tolker-Nielsen, Tim

2009. 75A(2):90-103


Time-Resolved Microscopy for Imaging Lanthanide Luminescence in Living Cells

Gahlaut, Nivriti; Miller, Lawrence W

2010. 77A(12):1113-1125


Photothermal Multispectral Image Cytometry for Quantitative Histology of Nanoparticles and Micrometastasis in Intact, Stained and Selectively Burned Tissues

Nedosekin, Dmitry A.; Shashkov, Evgeny V.; Galanzha, Ekaterina I.; Hennings, Leah; Zharov, Vladimir P.

2010. 77A(11):1049-1058


Evaluation of Intensity-Based Ratiometric FRET in Image Cytometry-Approaches and a Software Solution

Roszik, Janos; Lisboa, Duarte; Szollosi, Janos; Vereb, Gyoergy

2009. 75A(9):761-767


Abstracts of the 14th Leipziger Workshop: Cytomics and Regenerative Medicine and 7th International Workshop: Slide-Based Cytometry

Red Blood Cells Ageing, Characterized by, Vector Contrast Confocal Acoustic Scanning Microscopy
Mohamed, Ahmed E.; Zschoernig, O.; Willekens, F.; Kamanyi, A.; Von Buttlar, M.; Wannemacher, R.; Grill, W.
2009. 75A(8)712

Three-Dimensional Polar Representation for Multispectral Fluorescence Lifetime Imaging Microscopy

Leray, A.; Spriet, C.; Trinel, D.; Heliot, Laurent

2009. 75A(12)1007-1014


A Tool For Enhancement and Scoring of DNA Repair Foci

Gerashchenko, Bogdan I.; Dynlacht, Joseph R.

2009. 75A(3)245-252


Two-sided fluorescence resonance energy transfer for assessing molecular interactions of up to three distinct species in confocal microscopy

Fazekas, Zsolt; Petras, Miklos; Fabian, Akos; Palyi-Krekk, Zsuzsanna; Nagy, Peter; Damjanovich, Sandor; Vereb, Gyoergy; Szoellosi, Janos

2008. 73A(3)209-219


Comparative study of human erythrocytes by digital holographic microscopy, confocal microscopy, and impedance volume analyzer

Rappaz, Benjamin; Barbul, Alexander; Emery, Yves; Korenstein, Rafi; Depeursinge, Christian; Magistretti, Pierre J.; Marquet, Pierre

2008. 73A(10)895-903


Some new faces of membrane microdomains: A complex confocal fluorescence, differential polarization, and FCS imaging study on live immune cells

Gombos, Imre; Steinbach, Gabor; Pomozi, Istvan; Balogh, Andrea; Vaemosi, Gyoergy; Gansen, Alexander; Laszlo, Gloria; Garab, Gyozo; Matko, Janos

2008. 73A(3)220-229


Virtual Issue: Microscopy in Cytometry: Microscopy and High-Throughput Microscopy

Cytometry is a technology that uses optical and microscopic instrumentation to quantitatively unravel details from individual cells in cell culture. In this first of three virtual issues, we wanted to showcase recent microscopy-related articles in Cytometry part A from different research areas and disciplines. The focus in this issue will be on developed general advanced microscopy technologies or applications in high throughput microscopy. Happy reading!

Robert Zucker and Attila Tarnok


Constrained watershed method to infer morphology of mammalian cells in microscopic images

Nezamoddin N. Kachouie, Paul Fieguth, Darik Gamble, Eric Jervis, Zoheir Ezziane and Ali Khademhosseini

2010. 77A(12):1148-1159


Communicating subcellular distributions

Robert F. Murphy

2010. 77A(7):686-692


Neuron tracing in perspective

Erik Meijering

2010. 77A(7):693-704


Conditions for using FRAP as a quantitative technique—Influence of the bleaching protocol

Dominika O. Trembecka, Mateusz Kuzak and Jurek W. Dobrucki

2010. 77A(4):366-370


A novel imaging-based high-throughput screening approach to anti-angiogenic drug discovery

Lasse Evensen, David R. Micklem, Wolfgang Link and James B. Lorens

2010. 77A(1):41-51


A quantitative measure for alterations in the actin cytoskeleton investigated with automated high-throughput microscopy

Julian Weichsel, Nikolas Herold, Maik J. Lehmann, Hans-Georg Kräusslich and Ulrich S. Schwarz

2010. 77A(1):52-63


High content image cytometry in the context of subnuclear organization

W. H. De Vos, L. Van Neste, B. Dieriks, G. H. Joss and P. Van Oostveldt

2010. 77A(1):64-75


Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy

Quanli Wang, Jarad Niemi, Chee-Meng Tan, Lingchong You and Mike West

2010. 77A(1):101-110


Multispot live-image autofocusing for high-throughput microscopy of fluorescently stained bacteria

M. Zeder and J. Pernthaler

2009. 75A(9):781-788


Automated quantification of DNA demethylation effects in cells via 3D mapping of nuclear signatures and population homogeneity assessment

Arkadiusz Gertych, Kolja A. Wawrowsky, Erik Lindsley, Eugene Vishnevsky, Daniel L. Farkas and Jian Tajbakhsh

2009. 75A(7):569-583


A membrane-bound FRET-based caspase sensor for detection of apoptosis using fluorescence lifetime and total internal reflection microscopy

Brigitte Angres, Heiko Steuer, Petra Weber, Michael Wagner and Herbert Schneckenburger

2009. 75A(5):420-427


Going into lengths and widths, and depths—Microscopic cytomics quantifying cell function and cell communication

A.O.H. Gerstner and A. Tárnok

2009. 75A(4):279-281


Single-cell-based image analysis of high-throughput cell array screens for quantification of viral infection

Petr Matula, Anil Kumar, Ilka Wörz, Holger Erfle, Ralf Bartenschlager, Roland Eils and Karl Rohr

2009. 75A(4)309-318


Intensity calibration and automated cell cycle gating for high-throughput image-based siRNA screens of mammalian cells

Steven S. S. Poon, Jason T. Wong, Darren N. Saunders, Qianli C. Ma, Steven McKinney, John Fee and Samuel A. J. R. Aparicio

2008. 73A(10):904-917


High throughput FRET screening of the plasma membrane based on TIRFM

Christian Paar, Wolfgang Paster, Hannes Stockinger, Gerhard J. Schütz, Max Sonnleitner and Alois Sonnleitner

2008. 73A(5)442-450


A high-throughput system for segmenting nuclei using multiscale techniques

Prabhakar R. Gudla, K. Nandy, J. Collins, K. J. Meaburn, T. Misteli and S. J. Lockett

2008. 73A(5):451-466


Cell cycle studies based upon quantitative image analysis

Dennis W. Stacey and Masahiro Hitomi

2008. 73A(4):270-278


Automated classification of inflammation in colon histological sections based on digital microscopy and advanced image analysis

Levente Ficsor, Viktor Sebestyén Varga, Attila Tagscherer, Zsolt Tulassay and Bela Molnar

2008. 73A(3):230-237


Improved detection of branching points in algorithms for automated neuron tracing from 3D confocal images

Yousef Al-Kofahi, Natalie Dowell-Mesfin, Christopher Pace, William Shain, James N. Turner and Badrinath Roysam

2008.  73A(1):36-43


Virtual Issue: Microscopy in Cytometry: Image Cytometry

Cytometry is a technology that uses optical and microscopic instrumentation to quantitatively unravel details from individual cells in cell culture. In this second of three virtual issues, we are highlighting the best recent papers on image cytometry from Cytometry Part A.

Robert Zucker and Attila Tarnok



On the quantification of intracellular proteins in multifluorescence-labeled rat brain slices using slide-based cytometry

Reinert A, Mittag A, Reinert T, Tárnok A, Arendt T, Morawski M

2010. 77A(12):1148-1159


New Biomarkers Probing Depth of Cell Senescence Assessed by Laser Scanning Cytometry

Zhao, Hong; Halicka, H. Dorota; Traganos, Frank; Jorgensen, Ellen; Darzynkiewicz, Zbigniew

2010. 77A(12):1148-1159


Advances in cellular, subcellular, and nanoscale imaging in vitro and in vivo

Wessels JT, Yamauchi K, Hoffman RM, Wouters FS.

2010. 77A(12):1148-1159


NorthernLights in Slide-Based Cytometry and Microscopy

Wessels, J. T.; Busse, A. C.; Mahrt, J.; Hoffschulte, B.; Mueller, G. A.; Tarnok, A.; Mittag, A.

2010. 77A(12):1148-1159


Automated Multichannel Fluorescent Whole Slide Imaging and its Application for Cytometry

Varga, Viktor Sebestyen; Ficsor, Levente; Kamaras, Viktor; Jonas, Viktor; Virag, Tibor; Tulassay, Zsolt; Molnar, Bela

2010. 77A(12):1148-1159


Abstracts of the 14th Leipziger Workshop: Cytomics and Regenerative Medicine and 7th International Workshop: Slide-Based Cytometry

From Slides to Chips – Advancing Image Cytometry
Hennig, C.; Adams, N.; Hansen, G.
2010. 77A(12):1148-1159


Abstracts of the 14th Leipziger Workshop: Cytomics and Regenerative Medicine and 7th International Workshop: Slide-Based Cytometry

DNA Fluorescence as Trigger for Scanning Fluorescence Microscopy (SFM)
Mittag, A.; Marecka, M.; Malkusch, W.; Pierzchalski, A.; Bocsi, J.; Tarnok, A.
2010. 77A(12):1148-1159

SFMAC: A Novel Method for Analyzing Multiple Parameters on Lymphocytes with a Single Fluorophore in Cell-Microarray System

Tajiri, Kazuto; Kishi, Hiroyuki; Ozawa, Tatsuhiko; Sugiyama, Toshiro; Muraguchi, Atsushi

2010. 77A(12):1148-1159


A Versatile Platform for Comprehensive Chip-Based Explorative Cytometry

Hennig, Christian; Adams, Nico; Hansen, Gesine

2010. 77A(12):1148-1159


Quantification of Cardiomyocyte Contraction Based on Image Correlation Analysis

Kamgoue, A.; Ohayon, J.; Usson, Y.; Riou, L.; Tracqui, P.

2010. 77A(12):1148-1159


Flow and image cytometry side by side for the new frontiers in quantitative single-cell analysis

Tárnok A.

2010. 77A(12):1148-1159


Detection of Pathogenic E. coli O157:H7 by a Hybrid Microfluidic SPR and Molecular Imaging Cytometry Device

Zordan, Michael D.; Grafton, Meggie M. G.; Acharya, Ghanashyam; Reece, Lisa M.; Cooper, Christy L.; Aronson, Arthur I.; Park, Kinam; Leary, James F.

2010. 77A(12):1148-1159


Virtual Issue: What cytometrists really like to read

What cytometrists really like to read...
.. is what we hope to highlight in the very first virtual issue of Cytometry Part A . With our inaugural issue, "What cytometrists really like to read" and future virtual issues, we intend to showcase select papers of importance and interest to Cytometry Part A's readership as well as bring specific content tackling topical issues to your attention. Check back for new issues in the coming months!

In this issue, we bring you the top 20 most downloaded papers in Cytometry Part A since the beginning of 2009. Many of the papers, perhaps not surprisingly, deal with phenotyping and stem cells. In fact, 12 of the 20 most downloaded papers in the past 14 months are ones dedicated specifically to (polychromatic) immunophenotyping. This certainly reflects the growing relevance of the science of immunology for Cytometry Part A readers as well as the Journal's expanding position as the publication of choice in the field of immunology.

I hope that you will enjoy this first virtual issue and the many others to follow in the future.

With best regards,
Attila Tarnok
EiC, Cytometry Part A

Phenotype and function of human T lymphocyte subsets: Consensus and issues
Victor Appay, Rene A. W. van Lier, Federica Sallusto, Mario Roederer

Mouse hematopoietic stem cell identification and analysis
Grant A. Challen, Nathan Boles, Kuan-Yin K. Lin, Margaret A. Goodell

Nine-color flow cytometry for accurate measurement of T cell subsets and cytokine responses. Part I: Panel design by an empiric approach
Bridget E. McLaughlin, Nicole Baumgarth, Martin Bigos, Mario Roederer, Stephen C. De Rosa, John D. Altman, Douglas F. Nixon, Janet Ottinger, Carol Oxford, Thomas G. Evans, David M. Asmuth

Die hard: Are cancer stem cells the Bruce Willises of tumor biology?
Ákos Fábián, Márk Barok, György Vereb, János Szöllsi

"Small stem cells" in adult tissues: Very small embryonic-like stem cells stand up!
Ewa K. Zuba-Surma, Magdalena Kucia, Janina Ratajczak, Mariusz Z. Ratajczak

Circulating bone marrow-derived endothelial progenitor cells: Characterization, mobilization, and therapeutic considerations in malignant disease
Balazs Dome, Judit Dobos, Jozsef Tovari, Sandor Paku, Gabor Kovacs, Gyula Ostoros, Jozsef Timar

Tracking antigen-driven responses by flow cytometry: Monitoring proliferation by dye dilution
Paul K. Wallace, Joseph D. Tario Jr., Jan L. Fisher, Stephen S. Wallace, Marc S. Ernstoff, Katharine A. Muirhead

How many events is enough? Are you positive?
Mario Roederer

Stem cells of the adult cornea: From cytometric markers to therapeutic applications
Lili Takács, Enikö Tóth, András Berta, György Vereb

Cell cycle studies based upon quantitative image analysis
Dennis W. Stacey, Masahiro Hitomi

Endothelial progenitor cells: Implications for cardiovascular disease
Sven Möbius-Winkler, Robert Höllriegel, Gerhard Schuler, Volker Adams

Nine-color flow cytometry for accurate measurement of T cell subsets and cytokine responses. Part II: Panel performance across different
Bridget E. McLaughlin, Nicole Baumgarth, Martin Bigos, Mario Roederer, Stephen C. De Rosa, John D. Altman, Douglas F. Nixon, Janet Ottinger, Judy Li, Laurel Beckett, Barbara L. Shacklett, Thomas G. Evans, David M. Asmuth

Standardization and optimization of multiparameter intracellular cytokine staining
Laurel Nomura, Vernon C. Maino, Holden T. Maecker

A novel method based on click chemistry, which overcomes limitations of cell cycle analysis by classical determination of BrdU
Paolo Cappella, Fabio Gasparri, Maurizio Pulici, Jürgen Moll

MIFlowCyt: The minimum information about a flow cytometry experiment
Jamie A. Lee, Josef Spidlen, Keith Boyce, Jennifer Cai, Nicholas Crosbie, Mark Dalphin, Jeff Furlong, Maura Gasparetto, Michael Goldberg, Elizabeth M. Goralczyk, Bill Hyun, Kirstin Jansen, Tobias Kollmann, Megan Kong, Robert Leif, Shannon McWeeney, Thomas D. Moloshok, Wayne Moore, Garry Nolan, John Nolan, Janko Nikolich-Zugich, David Parrish, Barclay Purcell, Yu Qian, Biruntha Selvaraj, Clayton Smith, Olga Tchuvatkina, Anne Wertheimer, Peter Wilkinson, Christopher Wilson, James Wood, Robert Zigon, The International Society for Advancement of Cytometry Data Standards Task Force, Richard H. Scheuermann, Ryan R. Brinkman

Flow cytometry histograms: Transformations, resolution, and display
David Novo, James Wood

Intracellular Phospho-Flow cytometry reveals novel insights into TCR proximal signaling events. A comparison with Western blot
Anna Haas, Gisbert Weckbecker, Karl Welzenbach

Measuring Antigen-Specific Immune Responses, 2008 update
Jan W. Gratama, Florian Kern, Fabrizio Manca, Mario Roederer

Novel perspectives of neural stem cell differentiation: From neurotransmitters to therapeutics
Cleber A. Trujillo, Telma T. Schwindt, Antonio H. Martins, Janaína M. Alves, Luiz Eugênio Mello, Henning Ulrich

A new biomarker for mitotic cells
James W. Jacobberger, Phyllis S. Frisa, R. Michael Sramkoski, Tammy Stefan, Keith E. Shults, Deena V. Soni

Joint Virtual Issue on Stem Cells from Cytometry Part A, Cytometry Part B: Clinical Cytometry, Journal of Biophotonics, and Cell Proliferation

Cytometry Part A

Stromal Vascular Progenitors in Adult Human Adipose Tissue
Zimmerlin, Ludovic; Donnenberg, Vera S.; Pfeifer, Melanie E.; Meyer, E. Michael; Peault, Bruno; Rubin, J. Peter; Donnenberg, Albert D.

Phenotypes of Stem Cells from Diverse Origin
Tarnok, Attila; Ulrich, Henning; Bocsi, Jozsef

Human ESC Colony Formation Is Dependent on Interplay Between Self-Renewing hESCs and Unique Precursors Responsible for Niche Generation
Moogk, Duane; Stewart, Morag; Gamble, Darik; Bhatia, Mickie; Jervis, Eric

Optimal Reprogramming Factor Stoichiometry Increases Colony Numbers and Affects Molecular Characteristics of Murine Induced Pluripotent Stem Cells
Tiemann, Ulf; Sgodda, Malte; Warlich, Eva; Ballmaier, Matthias; Schoeler, Hans R.; Schambach, Axel; Cantz, Tobias

CD133 Positive Progenitor Endothelial Cell Lines from Human Cord Blood
Paprocka, Maria; Krawczenko, Agnieszka; Dus, Danuta; Kantor, Aneta; Carreau, Aude; Grillon, Catherine; Kieda, Claudine

ABCG2 is Required to Control the Sonic Hedgehog Pathway in Side Population Cells with Stem-like Properties
Balbuena, Jana; Pachon, Gisela; Lopez-Torrents, Guillermo; Aran, Josep M.; Castresana, Javier S.; Petriz, Jordi

Cytometry Part B: Clinical Cytometry

Electronic volume, aldehyde dehydrogenase, and stem cell marker expression in cells from human peripheral blood apheresis samples
Siddharth Sharma, Sherry Shariatmadar, Awtar Krishan

Localization of CD44 and CD90 positive cells to the invasive front of breast tumors
Vera S. Donnenberg, Albert D. Donnenberg, Ludovic Zimmerlin, Rodney J. Landreneau, Rohit Bhargava, Ryan A. Wetzel, Per Basse and Adam M. Brufsky

ALDH+/CD44+/CD24- expression in cells from body cavity fluids
Awtar Krishan, Deepti Sharma, Siddharth Sharma, Ronald M. Hamelik, Parvin Ganjei-Azar and Mehrdad Nadji

High CD133 expression levels in gastrointestinal stromal tumors
Fabio Bozzi, Elena Conca, Giacomo Manenti, Tiziana Negri, Silvia Brich, Alessandro Gronchi, Marco A. Pierotti, Elena Tamborini and Silvana Pilotti

Journal of Biophotonics

Label-free identification and characterization of human pluripotent stem cell-derived cardiomyocytes using second harmonic generation (SHG) microscopy
Samir Awasthi, Dennis L. Matthews, Ronald A. Li, Nipavan Chiamvimonvat, Deborah K. Lieu and James W. Chan

Two-photon microscopy of healthy, infarcted and stem-cell treated regenerating heart
Marika A. Wallenburg, Jun Wu, Ren-Ke Li and I. Alex Vitkin

Label-free biochemical characterization of stem cells using vibrational spectroscopy
James W. Chan and Deborah K. Lieu

In vivo imaging of hematopoietic stem cells and their microenvironment
Cristina Lo Celso, Juwell W. Wu and Charles P. Lin

The potential of biophotonic techniques in stem cell tracking and monitoring of tissue regeneration applied to cardiac stem cell therapy
Brian C. Wilson, I. Alex Vitkin and Dennis L. Matthews

Cell Proliferation

Multilineage differentiation of dental follicle cells and the roles of Runx2 over-expression in enhancing osteoblast/cementoblast-related gene expression in dental follicle cells
Pan K, Sun Q, Zhang J, Ge S, Li S, Zhao Y, Yang P.

Isolation of therapeutically functional mouse bone marrow mesenchymal stem cells within 3 h by an effective single-step plastic-adherent method
Hsiao F, Cheng C, Peng S, Huang H, Lian W, Jan M, Fang Y, Cheng K, Cheng W, Lin S, Wu S. Marino, M.

Long-term proliferation and characterization of human spermatogonial stem cells obtained from obstructive and non-obstructive azoospermia under exogenous feeder-free culture conditions
Lim J, Sung S, Kim H, Song S, Hong J, Yoon T, Kim J, Kim K, Lee D.

Cell proliferation of human bone marrow mesenchymal stem cells on biodegradable microcarriers enhances in vitro differentiation potential
Sun L, Hsieh D, Syu W, Li Y, Chiu H, Chiou T.

In vitro mesenchymal stem cell differentiation after mechanical stimulation
C. E. Sarraf, W. R. Otto and M. Eastwood