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

Introducing the Cytobank Webinar Series

Greetings Cytobank community!

We have launched a weekly webinar series designed to give you an overview of Cytobank functionality, where you will have the option to ask your burning Cytobank questions. We’ll present a brief overview of the platform in slide format, and then walk you through the analysis of an actual dataset using Cytobank. You’ll have the opportunity to privately ask your questions via the webinar chat box and we will address them at the end. The series will be on an alternating weekly schedule where we rotate covering basic analysis and advanced topics such as SPADE.

View the schedule of upcoming webinars on our Upcoming Meetings page.

- The Cytobank Team

April 21, 2014 at 7:26 pm Leave a comment

Cytobank User Stories: Kanutte Huse, Ph.D.

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 Kanutte Huse, Ph.D., a postdoctoral fellow at the Institute for Cancer Research, Oslo University Hospital, Norway. Currently, Kanutte is a visiting research fellow in the Irish lab at Vanderbilt University.

Send us feedback and let us know who you’d like to hear from (including yourself)!

What are you excited about in science? What is your scientific vision?
Kanutte Huse,

Kanutte Huse,
 Ph.D. Postdoctoral Fellow at Oslo University Hospital

The short answer is everything. I’m impressed by how natural scientists can measure and model everything around us, continuously increasing our knowledge about the world. More specifically, I’m interested in understanding the signaling networks of cells, and it fascinates me how seemingly simple signaling pathways can regulate a range of functional outcomes. I want to understand how alterations in signaling pathways lead to cancer. (more…)

April 7, 2014 at 7:28 pm Leave a comment

Cytobank User Stories: Stéphane Chevrier

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 Stéphane Chevrier, Ph.D., a Research Associate from the Institute of Molecular Life Sciences at University of Zurich.

Send us feedback and let us know who you’d like to hear from (including yourself)!

What are you excited about in science? What is your scientific vision?
Stéphane Chevrier,

Stéphane Chevrier, Ph.D.
University of Zurich

Science is particularly exciting because we have the opportunity to understand new biological processes with the potential of changing peoples’ lives. Therefore, I really appreciate working on translational projects. And when new technical advances or new biological tools enable us to address questions that could not be solved before, it becomes even more interesting!
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March 24, 2014 at 1:40 pm Leave a comment

Cytobank User Stories: Olga Ksionda, Ph.D.

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 Olga Ksionda, Ph.D., a postdoctoral scholar in the lab of Jeroen Roose in the Department of Anatomy at the UCSF School of Medicine. Send us feedback and let us know who you’d like to hear from (including yourself)!

What are you excited about in science? What is your scientific vision?
Olga Ksionda, Ph.D.

Olga Ksionda, Ph.D.
UCSF School of Medicine

I am very much interested in understanding the molecular aspects of T cell development, especially in pathological settings when wrong decisions are “made” and T cells become autoimmune or malignant.

In general terms, I have always found it fascinating when unrelated fields cross fertilize with unexpected outcomes. I consider some of the best examples of this the Cre system or recently described CRISPR technology.

(more…)

February 28, 2014 at 1:25 pm Leave a comment

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