Achieve better results, faster. Automate your end-to-end pipelines with the Cytobank Platform via The Cytobank API. The Cytobank API extends the power of the Cytobank Cloud to any software application. Now bench scientists can more seamlessly interact with computational biologists and reviewers to assess results of internal algorithms and pipelines.
Spitzer and Gherardini et al., from the Nolan Lab at Stanford University, report a novel bioinformatics approach to mapping the immune system called Scaffold (Single-Cell Analysis by Fixed Force- and Landmark-Directed).
Scaffold allows clustering of samples independently, thus allowing addition of new sample data over time. This approach requires users to develop or use a pre-defined reference map.
In their recent publication in Science, the authors reveal maps comparing immune organization among several tissue compartments, among mouse strains, between circadian states, and between species (mouse and human).
Come visit the Cytobank team at FOCiS and CYTO next week to learn more about what we’ve been up to, for some hands-on help, to share your wish list or just to chit-chat. We look forward to seeing you there!
Check out the various talks and posters at CYTO featuring Cytobank:
Saturday June 27, 2015
11:00 (Room: Alsh) – The First Multi-center Comparative Study Using a Novel Technology Mass Cytometry Time-of-Flight Mass Spectrometer (CyTOF2) for High-Speed Acquisition of Highly Multi-parametric Single Cell Data: A Status Report A. Nasaar, B. Carter, J. Lannigan, R. Montgomery, N. Paul, M. Poulin, K. Raddassi, A. Rahman and N. Rashidi. Yale Univ. Sch. of Med., Stanford Shared FACS Facilities, Univ. of Virginia Sch. of Med., Dana-Farber Cancer Inst., Fluidigm, Cambridge, MA, Icahn Sch. of Med. at Mount Sinai and Ragon Inst. of MGH, MIT and Harvard.
11:40 (Room: Alsh) – High Content Dissection of Human Melanoma Tumor Heterogeneity during Treatment Using Mass Cytometry J. Irish, D. Doxie, A. Greenplate, K. Diggins, H. Polikowsky, K. Dahlman, J. Sosman and M. Kelley. Vanderbilt Univ. Sch. of Med.
Always listening to our user feedback, we heard your requests to complete your viSNE workflow by overlaying Populations to uniquely color the viSNE continents. Our latest release brings you a new plot type configuration we call Dot Overlays that allows you to do this, and also lends itself to traditional back-gating approaches that allow you to see child populations in the context of ancestors.
Dot Overlays allow you to overlay not just Populations, but any of the Figure Dimensions within a single Dot Plot. Now you can compare Populations, Timepoints, Conditions, Individuals, and any dimension of your choosing within Dot Overlay plots. Just drag any figure dimension into the second (overlaid) position. See how your time course stacks out, compare your stimulations/titration data, or just see how populations sit in the context of each other (traditional back-gating). Visit our knowledge base for the full scoop on how to set up Dot Overlays, including a video tutorial.
Zunder and Finck et al., from the Nolan Lab at Stanford University report new cell barcoding reagents for mass cytometry that incorporate the previously unused element palladium, expanding the number of mass cytometry measurement parameters by six. Leveraging this methodology, they present a new barcoding scheme which can be used to identify and remove cell doublets, as well as provide software that deconvolves barcoded datasets via a “single-cell debarcode” algorithm .
The dataset for this paper is hosted and publicly available on Cytobank Community; a free resource for the analysis, workflow, and protocols represented in this paper. Cytobank is the cloud-based analytics platform for single cell analysis. In Cytobank you can easily access and analyze multi-parameter data, visualize findings, produce high-impact graphics, and securely connect and collaborate with colleagues around the world.
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.
Greg 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 . 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.
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 »