Forget Pixels: Adaptive Particle Representation of Fluorescence Microscopy Images

Bevan L. Cheeseman, Ulrik Gunther, Mateusz Susik, Krzysztof Gonciarz, Ivo F. Sbalzarini

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Apr 11, 2018

Received: 12th March 18

Modern microscopy modalities create a data deluge with gigabytes of data generated each second, or terabytes per day. Storing and processing these data is a severe bottleneck, not fully alleviated by data compression. We argue that this is because images are processed as regular grids of pixels. To address the root of the problem, we here propose a content-adaptive representation of fluorescence microscopy images called the Adaptive Particle Representation (APR). The APR replaces the regular grid of pixels with particles positioned according to image content. This overcomes storage bottlenecks, as data compression does, but additionally overcomes memory and processing bottlenecks, since the APR can directly be used in processing without going back to pixels. 

We present the ideas, concepts, and algorithms of the APR and validate them using noisy 3D image data. We show that the APR represents the content of an image while maintaining image quality. We then show that the adaptivity of the APR provides orders of magnitude benefits across a range of image processing tasks. Therefore, the APR provides a simple, extendable, and efficient content-aware representation of images that relaxes current data and processing bottlenecks.

Read in full at BioRxiv.

This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.

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