Adaptive Sampling for Storage of Progressive Images on DNA

TL;DR

This paper presents an innovative DNA-based image storage system utilizing adaptive sampling and progressive decoding, significantly reducing read costs and enabling efficient retrieval of resolution-specific images without PCR amplification.

Contribution

It introduces a novel DNA encoding scheme for progressive images that leverages adaptive sampling for targeted, cost-effective retrieval of specific image resolutions.

Findings

Reduces read cost for image retrieval in DNA storage.

Enables resolution-specific image decoding without PCR.

Improves reliability of DNA-based image storage systems.

Abstract

The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking for innovative media solutions that can store data over long time periods at a very low cost. DNA molecules, with their high density, long lifespan, and low energy needs, have emerged as a viable alternative to digital data archival. However, current DNA data storage technologies are facing challenges with respect to cost and reliability. Thus, coding rate and error robustness are critical to scale DNA storage and make it technologically and economically achievable. Moreover, the molecules of DNA that encode different files are often located in the same oligo pool. Without random access solutions at the oligo level, it is very impractical to decode a specific file from these mixed pools, as all oligos need to first be sequenced and decoded before a target file can be retrieved, which greatly deteriorates the read cost. This paper introduces a solution to efficiently encode and store images into DNA molecules, that aims at reducing the read cost necessary to retrieve a resolution-reduced version of an image. This image storage system is based on the Progressive Decoding Functionality of the JPEG2000 codec but can be adapted to any conventional progressive codec. Each resolution layer is encoded into a set of oligos using the JPEG DNA VM codec, a DNA-based coder that aims at retrieving a file with a high reliability. Depending on the desired resolution to be read, the set of oligos as well as the portion of the oligos to be sequenced and decoded are adjusted accordingly. These oligos will be selected at sequencing time, with the help of the adaptive sampling method provided by the Nanopore sequencers, making it a PCR-free random access solution.