December 31, 2012  |  Announcements

Cytobank Highlights from 2012

Dear Cytobank Community,

As 2012 draws to a close, we reflect on what on an exciting year it has been in cytometry. The benefits, uses, and applications of singe cell technologies (especially cytometry) were highlighted in various publications, including those by Bodenmiller et al and Behbehani et al using mass cytometry to profile cellular states [1, 2]. The era of high dimensional cytometry ushered by machines such as the CyTOF has enabled new explorations previously not possible. Emerging manuscripts such as these highlight a need for evolving algorithms for data analysis and visualization backed by the appropriate computation and infrastructure to handle this information. This is behind much of the vision that guides our roadmap and efforts as we launch into the new year.

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November 30, 2012  |  Announcements

Visually Annotate Plate Data to Accelerate Analysis

Researchers often choose to run data in 96- or 384-well plate format to increase the throughput of the acquisition process. The result is that it is easy to generate hundreds or thousands of files per experiment, and annotating these individually can be cumbersome. We’ve recently developed a Plate Annotator that allows users to annotate plate-associated files using a visual plate interface.

The Annotator allows users to annotate their data visually, selecting patterns of wells and applying annotations in bulk. Tagged files can then be arranged and re-arranged using standard Cytobank Illustrations tools to generate layouts of dot plots, histogram overlays, and heat maps among other visualizations.

The Plate Annotator is available on Fluidigm Cytobank and Enterprise Cytobank as a premium functionality.

Watch our demo video:

August 31, 2012  |  Announcements

Dose Response Analysis

Dose response analysis on data acquired with a single cell level of resolution can provide important insights into the behavior of specific cell subtypes that cannot be gleaned from bulk population studies. See the image below to compare dose response and EC50 values observed in bulk whole blood versus CD8+ T cells. Krutzik et al showed this in earlier work using signaling-based flow cytometry [1]. A recent article by Bodenmiller et al further demonstrates the power of dose response analysis in highly multiparametric datasets generated using mass cytometry (see Cytobank Report here) [2].

Dose Response Analysis of bulk PBMC compared to CD8+ T cells reveals the power of single cell resolution and mining data specific to subpopulations

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July 31, 2012  |  Announcements

Nolan Lab Signaling-Based Cytometry Resource

As part of educational and community outreach efforts in flow cytometry, the Nolan Lab at Stanford University has worked with the Cytobank team to launch a Signaling-Based (Fluorescence & Mass) Cytometry Resource. The Nolan lab has authored several key publications in flow cytometry on subjects including phosphoflow cytometry, barcoding, mass cytometry, and SPADE. Visit this Cytobank-powered resource to find experiment protocols for fluorescence and mass cytometry, Cytobank Reports, and Publications.

Experiment Protocols

The Experiment Protocols section of the resource links to protocols for fluorescence and mass cytometry, including those relevant to stimulations, barcoding, fix/perm methods, and titrating antibodies.

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June 14, 2012  |  Announcements

Cytobank Reports: Cisplatin Viability Stain for Mass Cytometry

The newest edition to our repertoire of Cytobank Reports is the work of Harris Fienberg, a Ph.D. candidate in Garry Nolan’s lab at Stanford University. Harris and colleagues developed a cisplatin-based viability stain for mass cytometry, which now allows researchers to discriminate between live and dead cells in mass cytometry experiments. You can visualize and analyze the raw data first hand on Cytobank. Click here to access the report.

You can also read more about Reports in general in our previous blog post on Cytobank Reports.

– Angela

June 11, 2012  |  Announcements

Upcoming meeting: CYTO 2012

CYTO 2012 is coming up later this month, and we thought we’d highlight some posters and talks.

Make sure to stop by the DVS Sciences booth (#412) to learn about Cytobank’s mass cytometry analysis resources, and visit the BD Biosciences booth (#101) for information on the Cytobank-powered FACSelect resource.

June 23-27, 2012
CYTO 2012
XXVII Congress of the International Society for Advancement of Cytometry (ISAC)
Congress Center Leipzig
Leipzig, Germany

Friday, June 22

Pre-Congress Course: Advanced Flow Cytometry Data Analysis

Module 2: Visualizing Data
Talk 2: Data Analysis in the Cloud: Community-based analyses, heat maps, SPADE – Jonathan M. Irish
10:45 – 11:05am

Module 4: Application-Oriented Data Analysis Issues
Talk 3: Phosphoantigens – Jonathan M. Irish
2:30 – 3:00pm
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May 5, 2012  |  Announcements

PDF Enhancements in Cytobank

On Cytobank, you can download the Illustrations you’ve built with our Print View and PDF tools. These are useful for generating figures for publications, printing for your lab notebook, and keeping a local copy of your Illustrations.

Our latest additions to this functionality include the ability for users to change the page size of PDFs such that large illustrations are no longer truncated horizontally.

Here is an overview of the changes:

Page formatting options

You can now select among a range of paper size options for PDFs, including three fixed-size options that constrain the page dimensions if you’re looking to print your plots (Letter, A4, and Poster) and two auto-fit options that scale the width and height of the PDF to exactly fit your document dimensions. The difference between the two auto-fit options has to do with limitations imposed by Adobe Acrobat Reader software, which will only open documents that do not exceed 200 inches in either dimension. So, if you plan on generating very large arrays of plots and want to use Adobe Acrobat Reader to view the PDF, you’ll need to select the “Very Large” auto-fit option, which inserts page breaks every 200 inches. If you do not want page breaks in your PDF and can use alternate software such as Adobe Illustrator to open your PDF, then choose the “Infinite” auto-fit option. With every page formatting option, if you choose a plot size and type combination that exceeds the width of the page format you have selected, an orange warning box will appear on the PDF generation page asking you to select a format with larger dimensions or to alter your plot size.

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