New kit helps researchers make sense of mass cytometry datasets to uncover cell subsets

February 8, 2017, Agency for Science, Technology and Research (A*STAR), Singapore
Cytofkit allows users to visualize the different subtypes of cells in their sample. Credit: A*STAR Singapore Immunology Network

A new software package offers easier analysis and interpretation of experiments that use mass cytometry, a sophisticated method for determining the properties of cells. The tool—called cytofkit—enables scientists to identify different subpopulations of cells within a sample of immune cells, cancer cells or other tissue types.

Flow cytometry remains the go-to method for biological investigations that require single-cell resolution. But, because the technology relies on fluorescent tags to detect different markers within the cell, only a limited number of labels can be applied before the light signals start to bleed into one another.

Mass cytometry helps solve this problem. By using metal labeling, the technique allows scientists to measure many more characteristics simultaneously within . But sorting through all the data it produces can be challenging, and most researchers agree that better analytic tools are needed.

Jinmiao Chen and her colleagues at the A*STAR Singapore Immunology Network made cytofkit in response to this need. The package combines state-of-the-art bioinformatics methods and in-house novel algorithms to help anyone make sense of mass cytometry data. "It provides a very user-friendly graphical interface and interactive visualization of analysis results," says Chen. "Anybody, including bench scientists and non-bioinformaticians, can use it without any training."

The involves four main steps: first, cytofkit performs data pre-processing according to the users' specifications; second, the software automatically identified different matching subsets of cells; third, it allows visualization of the data with color-labeled cell types; and lastly, it infers the relatedness between cell groups.

Chen's team tested the tool's performance on mass spectrometry results collected from a sample of . As they reported in PLOS Computational Biology, the software correctly identified known subpopulations of cells and further segregated these subsets to reveal additional cell types. In collaboration with A*STAR immunologist Evan Newell, the researchers also showed that cytofkit revealed many types of follicular helper T from blood and tonsils. Plus, says Chen, "we have tested the utility of cytofkit on a large number of other datasets not mentioned in the paper."

Cytofkit is also gaining popularity with scientists around the world. "It now has more than 4,000 users," says Chen. Her lab continues to improve and upgrade the tool in response to user feedback.

The software—which works both on flow and mass spectrometry datasets alike—is freely available through Bioconductor, an open-source software framework for biologists. It can be found here.

Explore further: Intuitive and efficient solution to eliminate anomalies in immunological studies

More information: Hao Chen et al. Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline, PLOS Computational Biology (2016). DOI: 10.1371/journal.pcbi.1005112

Related Stories

Recommended for you

Scientists ID another possible threat to orcas: pink salmon

January 19, 2019

Over the years, scientists have identified dams, pollution and vessel noise as causes of the troubling decline of the Pacific Northwest's resident killer whales. Now, they may have found a new and more surprising culprit: ...

Researchers come face to face with huge great white shark

January 18, 2019

Two shark researchers who came face to face with what could be one of the largest great whites ever recorded are using their encounter as an opportunity to push for legislation that would protect sharks in Hawaii.

Why do Hydra end up with just a single head?

January 18, 2019

Often considered immortal, the freshwater Hydra can regenerate any part of its body, a trait discovered by the Geneva naturalist Abraham Trembley nearly 300 years ago. Any fragment of its body containing a few thousands cells ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.