viSNE now available on Cytobank

The Cytobank team has been working diligently to provide top tier analysis solutions for our users; viSNE in Cytobank is our most recent addition and we are very excited about what it has to offer.

What is viSNE? And how does it work?

viSNE is a tool for reducing high-parameter data down to two dimensions, making it easy for scientists to not only visually identify interesting and rare biological subsets, but also gate single cell events across different samples.

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November 13, 2014 at 10:51 pm Leave a comment

Behbehani et al. Transient Partial Permeabilization with Saponin Enables Cellular Barcoding Prior to Surface Marker Staining.

Greg BehbehaniGreg Behbehani, a physician scientist, is focused on translational research, leveraging his work treating patients in clinical trials for high-risk hematologic malignancies towards the ultimate goal of utilizing data generated in the laboratory to predict ideal chemotherapy regimens and optimal novel agents for individual patients.

Most recently Dr. Behbehani has contributed to a published paper surrounding research of new protocols for barcoding on mass and fluorescence cytometry [1]. The dataset is hosted and publicly available on Community Cytobank; a free resource for individuals interested in the analysis, workflow, and protocols represented in this paper.

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November 10, 2014 at 1:04 pm Leave a comment

Cytobank User Stories: Gabi Fragiadakis

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of fluorescence and mass cytometry.

This time we interview Gabi Fragiadakis, Ph.D. candidate in the Nolan Lab at Stanford University School of Medicine.

What are you excited about in science? What is your scientific vision?
Gabi Fragiadakis


Gabi Fragiadakis
Ph.D. candidate at Stanford University School of Medicine

We are in a particularly exciting time for immunology—with the advent of new technologies, we have the potential to profile the immune system as a dynamic set of interactions as opposed to looking at one piece at a time.

I believe that the ability to examine the immune system as a system will lead to vast improvements in patient monitoring and treatment.
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September 24, 2014 at 5:06 pm Leave a comment

Cytobank User Stories: Marianne Enger

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of fluorescence and mass cytometry.

This time we interview Marianna Enger, the flow cytometry core facility manager at University of Bergen.

What are you excited about in science? What is your scientific vision?
Marianna Enger


Marianna Enger
Flow Cytometry Core Facility Manager at University of Bergen

My vision as a flow cytometry core facility manager is to make flow cytometry available and affordable to anyone interested. The ambition is to provide research groups with the specialized resources and the expertise they need to produce the best possible scientific output in a cost effective way.

Cell signaling pathways interact with one another to form networks and my special interest is in hematopietic stem cells and signaling pathways. Flow cytometry is great for exploring signaling networks which I find very challenging and exciting and my wishes for the future include a CyTOF. My focus for the last two years has been on normal hematopoietic cellular responses and their potential disregulation in disease.

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July 21, 2014 at 2:43 pm Leave a comment

Population Sunbursts: Dynamically interact with population hierarchies and statistics

Communicating population relationships and associated statistical data is a fundamental aspect of single cell data analysis. A common method of communicating population relationships is via data tables that list populations and statistics. However, this becomes cumbersome as researchers work with higher dimensional experiments and complex gating strategies. To address this challenge, we’ve added a Sunburst Visualization that allows users to visually communicate population hierarchies. 

Think of a Sunburst as a radial tree where ‘wedges’ represent populations. The root of the tree in the center, descendants expand outward as slices of concentric rings, and each ring represents a level of your hierarchy. The size of a wedge is proportionate to the number of events in the population, and mousing over any wedge reveals statistical information.  Users can start with a global view of their gating hierarchy and then interactively drill down to the subsets in which they are interested.

The Sunburst visualization is available on Premium and Enterprise Cytobank sites, at the bottom of the gating page.

June 20, 2014 at 1:32 pm Leave a comment

FCS File Quality Control Validation

With the recent rise in cytometry data post-processing (e.g., normalization, debarcoding, concatenation), we at Cytobank have seen many FCS files that do not conform to the ISAC specification, and some of these variations in file writing may lead to downstream errors. As a result, we’ve implemented a Quality Control validator, built into Cytobank, that determines the compliance of your FCS files compared with the specification.

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April 30, 2014 at 4:59 pm Leave a comment

The analysis challenges of high dimensional cytometry

With the rise in high dimensional cytometry, the need for new ways of managing and analyzing this information is essential. The Cytobank approach and platform led to several key publications in this area. As a result, we were invited to contribute a chapter published in Current Topics in Microbiology and Immunology. This chapter highlights the needs for new approaches to work with high dimensional cytometry and uses the Cytobank platform as an example of addressing the challenges. In addition, we also provide some practical ways of using algorithms such as SPADE to analyze datasets.
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April 22, 2014 at 7:57 pm Leave a comment

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