Sunday, December 5, 2021

‘Analysis pipeline’ provides rapid insight into how cells are changed by disease

A new “image analysis pipeline” is giving scientists rapid new insight into how disease or injury have changed the body, down to the individual cell, reports Tech Xplore. It’s called TDAExplore, which takes the detailed imaging provided by microscopy, pairs it with a hot area of mathematics called topology, which provides insight on how things are arranged, and the analytical power of artificial intelligence to give, for example, a new perspective on changes in a cell resulting from ALS and where in the cell they happen, says Dr. Eric Vitriol, cell biologist and neuroscientist at the Medical College of Georgia. It is an “accessible, powerful option” for using a personal computer to generate quantitative – measurable and consequently objective – information from microscopic images that likely could be applied to other standard imaging techniques such as X-rays and PET scans, they report in the journal Patterns. “We think this is exciting progress into using computers to give us new information about how image sets are different from each other,” Vitriol says. “What are the actual biological changes that are happening, including ones that I might not be able to see, because they are too minute, or because I have some kind of bias about where I should be looking.” At least in the analysing data department, computers have our brains beat, the neuroscientist says, not just in their objectivity but in the amount of data they can assess. Computer vision, which enables computers to pull information from digital images, is a type of machine learning that has been around for decades, so he and his colleague and fellow corresponding author Dr. Peter Bubenik, a mathematician at the University of Florida and an expert on topological data analysis, decided to partner the detail of microscopy with the science of topology and the analytical might of AI. Topology and Bubenik were key, Vitriol says. Topology is “perfect” for image analysis because images consist of patterns, of objects arranged in space, he says, and topological data analysis (the TDA in TDAExplore) helps the computer also recognize the lay of the land, in this case where actin – a protein and essential building block of the fibres, or filaments, that help give cells shape and movement – has moved or changed density. It’s an efficient system, that instead of taking literally hundreds of images to train the computer how to recognize and classify them, it can learn on 20 to 25 images. Part of the magic is the computer is now learning the images in pieces they call patches. Breaking microscopy images down into these pieces enables more accurate classification, less training of the computer on what “normal” looks like, and ultimately the extraction of meaningful data, they write. The published study provides all the pieces for other scientists to use TDAExplore.

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