June 20, 2014  |  Uncategorized

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.

November 1, 2013  |  Uncategorized

Cytobank Remembers Leonard Herzenberg

Leonard ‘Len’ Herzenberg, a world renowned scientist, innovator, and mentor, passed away on October 27 at the age of 81 after a brief illness. In cooperation with his wife and scientific partner, Lee Herzenberg, he brought the power of flow cytometry to the field of immunology, developed fluorescence activated cell sorting, and mentored some of the most influential figures in flow cytometry today – including Garry Nolan, out of whose lab Cytobank was formed.

Several of us at Cytobank have spent time at the Stanford Shared FACS Facility working on projects and can intimately appreciate Len Herzenberg’s contributions to the field in both instrumentation and the pervasive attitude of openness. The cytometry community has always been open and inclusive – labs and core facilities strive to educate new users and spread cytometry expertise as far as possible. These ideals were instilled in the community by the founders and pioneers of flow cytometry, and Len played a large role in the process. This was evident in the way he handled the distribution of early hybridomas (a term he coined during a sabbatical in César Milstein’s laboratory) – open and available to anyone who asked.

As we reflect on Len’s contributions to the field, we’d like to highlight a memorial written by Mario Roederer and a video interview  performed by him of both Lee and Len Herzenberg. If you’d like to read more about Lee and Len’s life and scientific journey from Brooklyn College, to Cal Tech, the Pasteur Institute, the NIH, and then finally to Stanford, please visit their lab’s website where the article “A Tale of Two Lives Intertwined” is hosted.

Our condolences go out to Lee and the rest of the Herzenberg family – the world has lost a great man and he’ll be missed, both in the corridors of Stanford and in the scientific community at large.

[Edit-Dec2013] We’d like to likewise share a thoughtful memorial of Len Herzenberg offered by Garry Nolan.

March 29, 2013  |  Education, Uncategorized

Data Management Discussion Panel

As you’ve probably heard from us before, the era of Big Data is here and we want to make sure you’re prepared to face the unique challenges it brings. However, we at Cytobank aren’t the only ones thinking about the implications of managing all the data being generated by high dimensional flow and mass cytometry; +Ryan Duggan via the Cytometry Google community recently hosted a Cytometry Hangout on the topic of Data Management and had a guest panel consisting of our very own Nikesh Kotecha, Kevin Krouse from labkey.org, and Wade Rogers from the University of Pennsylvania. If you didn’t happen to catch it live, below is a quick summary of the panel.

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February 28, 2013  |  Education, Uncategorized

My First CyTOF Experiment

Having recently joined Cytobank and with little practical experience with the CyTOF, I headed over to the Nolan lab to do my very first CyTOF experiment. Every year, the Nolan lab hosts a phospho-flow course where a group of interested researchers fly to Stanford to learn how to perform a phospho-flow experiment. During my day there, I used a protocol in development for this course to generate data on the CyTOF and subsequently used  Premium Cytobank for analysis. This is a record of my experiences that will hopefully be helpful to those of you just starting out in the world of mass cytometry as well.

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