An image-to-answer algorithm for fully automated digital PCR image processing

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26620%2F22%3APU145666" target="_blank" >RIV/00216305:26620/22:PU145666 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00064165:_____/22:10442785 RIV/00216208:11110/22:10442785

Výsledek na webu

<a href="https://pubs.rsc.org/en/content/articlelanding/2022/LC/D1LC01175H" target="_blank" >https://pubs.rsc.org/en/content/articlelanding/2022/LC/D1LC01175H</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1039/d1lc01175h" target="_blank" >10.1039/d1lc01175h</a>

Jazyk výsledku

angličtina

Název v původním jazyce

An image-to-answer algorithm for fully automated digital PCR image processing

Popis výsledku v původním jazyce

The digital polymerase chain reaction (dPCR) is an irreplaceable variant of PCR techniques due to its capacity for absolute quantification and detection of rare deoxyribonucleic acid (DNA) sequences in clinical samples. Image processing methods, including micro-chamber positioning and fluorescence analysis, determine the reliability of the dPCR results. However, typical methods demand high requirements for the chip structure, chip filling, and light intensity uniformity. This research developed an image-to-answer algorithm with single fluorescence image capture and known image-related error removal. We applied the Hough transform to identify partitions in the images of dPCR chips, the 2D Fourier transform to rotate the image, and the 3D projection transformation to locate and correct the positions of all partitions. We then calculated each partition's average fluorescence amplitudes and generated a 3D fluorescence intensity distribution map of the image. We subsequently corrected the fluorescence non-uniformity between partitions based on the map and achieved statistical results of partition fluorescence intensities. We validated the proposed algorithms using different contents of the target DNA. The proposed algorithm is independent of the dPCR chip structure damage and light intensity non-uniformity. It also provides a reliable alternative to analyze the results of chip-based dPCR systems.

Název v anglickém jazyce

An image-to-answer algorithm for fully automated digital PCR image processing

Popis výsledku anglicky

The digital polymerase chain reaction (dPCR) is an irreplaceable variant of PCR techniques due to its capacity for absolute quantification and detection of rare deoxyribonucleic acid (DNA) sequences in clinical samples. Image processing methods, including micro-chamber positioning and fluorescence analysis, determine the reliability of the dPCR results. However, typical methods demand high requirements for the chip structure, chip filling, and light intensity uniformity. This research developed an image-to-answer algorithm with single fluorescence image capture and known image-related error removal. We applied the Hough transform to identify partitions in the images of dPCR chips, the 2D Fourier transform to rotate the image, and the 3D projection transformation to locate and correct the positions of all partitions. We then calculated each partition's average fluorescence amplitudes and generated a 3D fluorescence intensity distribution map of the image. We subsequently corrected the fluorescence non-uniformity between partitions based on the map and achieved statistical results of partition fluorescence intensities. We validated the proposed algorithms using different contents of the target DNA. The proposed algorithm is independent of the dPCR chip structure damage and light intensity non-uniformity. It also provides a reliable alternative to analyze the results of chip-based dPCR systems.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10405 - Electrochemistry (dry cells, batteries, fuel cells, corrosion metals, electrolysis)

Projekt

<a href="/cs/project/LTACH19005" target="_blank" >LTACH19005: Vysoce přesný systém digitální polymerázové řetězové reakce pro detekci cfDNA pro neinvazivní prenatální testování (NIPT</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2022

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

LAB ON A CHIP

ISSN

1473-0197

e-ISSN

1473-0189

Svazek periodika

22

Číslo periodika v rámci svazku

7

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

11

Strana od-do

1333-1343

Kód UT WoS článku

000765868800001

EID výsledku v databázi Scopus

2-s2.0-85124137073