Announcing flowCAP - Flow Cytometry: Critical Assessment of Population Identification Methods

[Ryan Brinkman]

We are pleased to announce the opening of the first set of flowCAP challenges. The goal of flowCAP is to assess computational approaches for the identification of cell populations of interest in flow cytometry data. This problem is very close to the clustering problem in machine learning.

Flow cytometry has been widely used by immunologists and cancer biologists for more than 30 years as a biomedical research tool to distinguish different cell types in mixed populations based on the expression of cellular markers. It has also become a widely used diagnostic tool for clinicians to identify abnormal cell populations associated with disease. In the last decade, advances in instrumentation and reagent technologies have enabled simultaneous single-cell measurement of tens of surface and intracellular markers, as well as tens of signaling molecules, positioning flow cytometry to play an even greater role in medicine and systems biology. However, the rapid expansion of flow cytometry applications has outpaced the functionality of traditional analysis tools used to interpret flow cytometry data such that scientists are faced with the daunting prospect of manually identifying interesting cell populations in 20 dimensional data from a collection of millions of cells. For this reason a reliable automated approach to flow cytometric analysis is desirable. While there has been a growing interest among the scientific community in developing such methods, guidance for end users about appropriate use and application of these methods is scarce.

In response to this need, we are conducting the Flow Cytometry: Critical Assessment of Population Identification Methods (flowCAP) challenge. The first set of flowCAP challenges provide the means to objectively test approaches for the identification of cell populations of interest in flow cytometry data by comparison to manual analysis by experts using common datasets. Datasets and challenge guidelines are now available at http://flowcap.flowsite.org.

Time Line

Release of materials for challenge 1 and 2: 01 MAR 2010
Submission deadline for challenge 1 and 2: 14 JUN 2010
Release of materials for challenge 3: 14 JUN 2010
Submission deadline for challenge 3: 07 JUL 2010
Release of materials for challenge 4: 07 JUL 2010
Submission deadline for challenge 4: 01 AUG 2010
Public release of the results: 01 SEP 2010
flowCAP summit: During the last weeks of September 2010

Summit

An NIH/NIAID-sponsored summit will be held at the NIH campus during the last weeks of September 2010 for two days. flowCAP participants (travel will be subsidized) and users will be invited to present their work and participate in group discussion.

Cheers,
Ryan Brinkman on behalf of the the flowCAP Organizing Committee:

Ryan Brinkman, British Columbia Cancer Agency
Raphael Gottardo, Clinical Research Institute of Montreal
Richard H. Scheuermann, University of Texas Southwestern Medical Center
Jill Schoenfeld, TreeStar Inc.