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An open-source robotic platform that enables automated monitoring of replicate biofilm cultivations using optical coherence tomography.

ABSTRACT: The paper introduces a fully automated cultivation and monitoring tool to study biofilm development in replicate experiments operated in parallel. To gain a fundamental understanding of the relation between cultivation conditions and biofilm characteristics (e.g., structural, mechanical) a monitoring setup allowing for the standardization of methods is required. Optical coherence tomography (OCT) is an imaging modality ideal for biofilms since it allows for the monitoring of structure in real time. By integrating an OCT device into the open-source robotic platform EvoBot, a fully automated monitoring platform for investigating biofilm development in several flow cells at once was realized. Different positioning scenarios were tested and revealed that the positioning accuracy is within the optical resolution of the OCT. On that account, a reliable and accurate monitoring of biofilm development by means of OCT has become possible. With this robotic platform, reproducible biofilm experiments including a statistical analysis are achievable with only a small investment of operator time. Furthermore, a number of structural parameters calculated within this study confirmed the necessity to perform replicate biofilm cultivations.

SUBMITTER: Gierl L

PROVIDER: S-EPMC7113294 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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An open-source robotic platform that enables automated monitoring of replicate biofilm cultivations using optical coherence tomography.

Gierl Luisa L Stoy Kasper K Faíña Andrés A Horn Harald H Wagner Michael M

NPJ biofilms and microbiomes 20200401 1

The paper introduces a fully automated cultivation and monitoring tool to study biofilm development in replicate experiments operated in parallel. To gain a fundamental understanding of the relation between cultivation conditions and biofilm characteristics (e.g., structural, mechanical) a monitoring setup allowing for the standardization of methods is required. Optical coherence tomography (OCT) is an imaging modality ideal for biofilms since it allows for the monitoring of structure in real ti ...[more]

PMID: 32238809

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Project description:ObjectiveTo develop an algorithm for automated quantification of Haller's layer in choroid using swept-source optical coherence tomography (OCT).BackgroundSo far, to understand the association of various diseases with structural changes of choroid, only gross indicators such as thickness, volume and vascularity index have been examined. However, certain diseases affect specific sublayers of the choroid. Accordingly, a need for targeted quantitation arises. In particular, there is significant interest in understanding Haller's layer, a choroidal sublayer comprising relatively large blood vessels. Unfortunately, its intricate vasculature makes, manual quantitation difficult, tedious, and error-prone. To surmount this difficulty, it is imperative to develop an algorithmic method.MethodologyThe primary contribution of this work consists in developing an approach for detecting the boundary between Haller's and Sattler's layers, the latter comprising medium-sized vessels. The proposed algorithm estimates vessel cross-sections using exponentiation-based binarization, and labels a vessel large if its cross-section exceeds certain statistically determined threshold. Finally, the desired boundary is obtained as a smooth curve joining the innermost points of such large vessels. On 50 OCT B-scans (of 50 healthy eyes), our algorithm was validated both qualitatively and quantitatively, by comparing with intra-observer variability. Extensive statistical analysis was performed using metrics including Dice coefficient (DC), correlation coefficient (CC) and absolute difference (AD).ResultsThe proposed algorithm achieved a mean DC of 89.48% (SD:5.03%) in close agreement with the intra-observer repeatability of 89.12% (SD:5.68%). Corresponding mean AD and mean CC were of 17.54 ?m (SD:16.45?m) and 98.10% (SD:1.60%) which too approximate the respective intra-observer repeatability values 19.19 ?m (SD:17.69 ?m) and 98.58% (SD:1.12%).ConclusionHigh correlation between algorithmic and manual delineations indicates suitability of our algorithm for clinically analyzing choroid in greater finer details, especially, in diseased eyes.

Dataset Information

An open-source robotic platform that enables automated monitoring of replicate biofilm cultivations using optical coherence tomography.

Publications

An open-source robotic platform that enables automated monitoring of replicate biofilm cultivations using optical coherence tomography.

Similar Datasets

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