Abstract
Mass Based Imaging (MBI) technologies such as Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and Imaging Mass Cytometry (IMC) allow for the simultaneous measurement of the expression levels of 40 or more proteins in biological tissue, providing insight into cellular phenotypes and organization in situ. Imaging artifacts, resulting from the sample, assay or instrumentation complicate downstream analyses and require correction by domain experts. Here, we present MBI Analysis User Interface (MAUI), a series of graphical user interfaces that facilitate this data pre-processing, including the removal of channel crosstalk, noise and antibody aggregates. Our software streamlines these steps and accelerates processing by enabling real-time and interactive parameter tuning across multiple images.
Highlights
A major goal of biological research and medical diagnosis is to understand how cellular phenotypes at a single cell level relate to the multi-cellular structures in which they reside
We present MAUI (MBI Analysis User Interface), a graphical user interface that wraps a series of image processing methods to eliminate imaging artifacts in Mass Based Imaging (MBI)
MAUI was designed for MBI methods, such as Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and Imaging Mass Cytometry (IMC), we demonstrate its utility for fluorescent-based imaging
Summary
High-dimensional Imaging technologies allow to simultaneously measure the expression levels of dozens of proteins in biological tissue, providing insight into single-cell phenotypes and organization in situ. Imaging artifacts, resulting from the sample, assay or instrumentation complicate downstream analyses and require correction by domain experts. We present MAUI, a series of graphical user interfaces that facilitate this data pre-processing, including the removal of channel crosstalk, noise and antibody aggregates. MAUI accelerates and automates these steps, such that reproducible, highquality data will be the input for subsequent stages of analysis. This is a PLOS Computational Biology Software paper
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