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.

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

Cytobank User Stories: Hervé Luche, 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 Hervé Luche, Ph.D., R&D Manager at the Centre d’Immunophénomique in Marseilles, France.

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?
Herve Luche,

Herve Luche, Ph.D.

I am very much interested in trying to understand how cells integrate signals and communicate with their environment to actually change their transcriptional programs, fate or acquire a new function. To try to tackle down this complexity in biology, one necessarily needs multi-disciplinary approaches and to combine multiple-expertise. I like sharing ideas with other people of different scientific backgrounds to establish new models and theories. The most exciting part of the work to me is when you bring all pieces of the puzzle together and that your model becomes partly true and clarifies one scientific question. It does not happen very often (to me at least!) but when it does, it is great fun!
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January 23, 2014 at 3:00 pm Leave a comment

Cytobank 3.0: Enhanced gating, upload, and download

Cytobank 3.0 marks a new chapter in our journey where users can now enjoy a streamlined upload, download, and gating experience. We’d like to take this opportunity to introduce you to what’s new:

Uploading and Downloading

Data upload and download have a new interface, and the old Java applets have been retired. This means faster uploading and downloading and fewer compatibility issues.

We’ve also added mechanisms for users to upload ACS and ZIP files, and have expanded the prevalence and detail-level of progress bars. Want to easily transfer experiments between your accounts on different Cytobank servers? Users can now export ACS versions of their experiments from the Experiment Details page and use ACS upload to move them over.

Enhanced Gating Interface

Like upload and download, gating has received a makeover and no longer uses Java. The first thing you’ll notice is improved loading time and fewer compatibility issues. The new interface also includes several frequently-requested enhancements, including axis tick marks, display of gate percentages, marking of tailored gates (T), marking of hidden gates (H), display of both channel short names and long names, and an expandable plot scales section. (more…)

January 21, 2014 at 5:31 pm Leave a comment

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