Software and Informatics

Guides, FAQs, and protocols to help you get the most out of your system

Frequently Asked Questions

What is IsoSpeak?

IsoSpeak is a software package for IsoLight data analysis. It provides a comprehensive suite of tools for the downstream analysis of single-cell data obtained through the IsoLight platform. It is fully integrated with the IsoLight, allowing you to plan your project setup prior to an IsoLight run, and requires under 30 minutes per experiment to reveal your high-dimensional, single-cell results. The IsoSpeak suite of user-friendly and intuitive bioinformatics tools are designed to explore, characterize the single-cell, polyfunctional profiles of each experiment, and characterize single-cell level differences across samples

Do I need to be a bioinformatician to process and analyze my high-throughput data?

No! Our IsoSpeak software fully automates data processing and allows the user to generate publication-ready figures in no time. It is designed to be intuitive and does not require a bioinformatics or statistics background to use. Please check back soon for a brief video demonstration of the IsoSpeak software.

What kind of statistical analysis is performed by the IsoSpeak software?

IsoSpeak lets you visualize data in many forms, including functional heat maps, polyfunctional activation topology (PAT) PCA visualizations, and rank-ordered polyfunctional strength index (PSI) bar graphs. Furthermore, data can be exported as csv or tab-delimited text files to allow for analysis with your own favorite tools.

How can I buy your software?

IsoSpeak comes free of charge with the purchase of an IsoLight, and is provided on a standalone laptop. At the moment, we do not sell IsoSpeak licenses separately.

What are the storage requirements for IsoCode or CodePlex data?

Roughly 8GB of raw data is generated per IsoCode or CodePlex chip. The IsoLight has networking capabilities and we recommend pushing your data to a server for storage and backup, and for direct access using our IsoSpeak software. Alternatively, data can be exported from the IsoLight using a USB drive and analyzed on the supplied IsoSpeak laptop.

How does IsoSpeak distinguish between background noise and true cytokine secretions?

The background noise levels are determined per analyte on each chip by processing the image data generated on the IsoLight. The software analyzes the fluorescence intensity in ~1000 empty "zero-cell" microchambers on the same chip. A cutoff equal to the average background intensity plus three times the standard deviation is used to determine which readouts are true cytokine secretions and which ones are not.