Microbial single-cell analysis in picoliter-sized batch cultivation chambers

Kaganovitch, Eugen; Steurer, Xenia; Doğan, Deniz; Probst, Christopher; Wiechert, Wolfgang; Kohlheyer, Dietrich

doi:10.1016/j.nbt.2018.01.009

Cited by 26 publications

(17 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Cultivation took place inside a special microfluidic cultivation device. 30 The assembled training and test sets are available online at https://doi.org/10.5281/zenodo.6497715.…”

Section: Datamentioning

confidence: 99%

microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation

Scherr

Seiffarth

Wollenhaupt

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

In biotechnology, cell growth is one of the most important properties for the characterization and optimization of microbial cultures. Novel live-cell imaging methods are leading to an ever better understanding of cell cultures and their development. The key for analyzing acquired data is accurate and automated cell segmentation at the single-cell level. Therefore, we present microbeSEG, a user-friendly cell segmentation tool with OMERO data management. microbeSEG utilizes a state-of-the-art deep learning-based segmentation method and can be used for instance segmentation of a wide range of cell morphologies and imaging techniques, e.g., phase contrast or fluorescence microscopy. The main focus of microbeSEG is a comprehensible, easy, efficient, and complete workflow from creation of training data to final application of the trained segmentation model. We demonstrate that accurate cell segmentation results can be obtained within 45 minutes of user time. Utilizing public segmentation data sets or pre-labeling further accelerates the microbeSEG workflow. This opens the door for accurate and efficient data analysis of microbial cultures.

show abstract

“…Cultivation took place inside a special microfluidic cultivation device. 30 The assembled training and test sets are available online at https://doi.org/10.5281/zenodo.6497715.…”

Section: Datamentioning

confidence: 99%

microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation

Scherr

Seiffarth

Wollenhaupt

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Microreactor technology has evolved significantly from analytical applications to the production of chemicals and reaction kinetics advancements, attracting academia and industries' attention due to its unique flow, mixing, and separation features 1, 2. The micro‐sized reactors have been utilized in different chemical, pharmaceutical, biotechnology, and even environmental fields 3–9, due to the unique microflow environment provided, which enables controlling the quality of the final product 10–13. The miniature microreactors offer high‐throughput methods in chemical synthesis with higher yield and selectivity, improving the sample consistency at lower reaction volume 14 with lower energy consumption 15–23,] thus providing a platform in synthesizing important and rare materials.…”

Section: Introductionmentioning

confidence: 99%

Heterogeneous Microfluidic Reactors: A Review and an Insight of Enzymatic Reactions

2022

View full text Add to dashboard Cite

Heterogeneous reactions are considered the heart of chemical synthesis with numerous industrial applications due to their high conversion rates and low reaction time. On the other hand, the performance of heterogeneous reactions suffers from several drawbacks such as lower product selectivity and high mass transfer resistance that, in many cases, reduce the reaction rate. The efficiency of various conventional mixing techniques in heterogeneous reactors is believed to play a critical role in controlling the product quality and mass transfer rates besides other essential factors. Microfluidics technology provides a unique opportunity to revisit many established heterogeneous reaction processes to optimize and understand the reaction mechanisms. The unique flow conditions in microflow systems provide an excellent platform for exploring the effect of high‐precision micromixing techniques on reaction rates and productivities. Recent advances in microreactor technology in general and specifically heterogeneous reactions in microflow systems with an insight on the enzymatic reactions in microreactors are reviewed.

show abstract

“…Microfluidic devices are miniaturized fluid and gas control systems developed for various applications in chemistry and biology such as lab on a chip (LOC) or micro total analysis systems (µTAS) [1,2], genetic analysis [3], cell analysis [4], organs on chips [5], drug discovery [6], and biosensing [7,8]. Polydimethylsiloxane (PDMS) is the most commonly used material for microfluidic devices [9][10][11][12][13][14][15][16][17]. PDMS-based microfluidic devices are typically fabricated by bonding a soft lithography-processed PDMS piece on a substrate such as glass, silicon, or PDMS.…”

Section: Introductionmentioning

confidence: 99%

Fabrication and Demonstration of a 3D-printing/PDMS Integrated Microfluidic Device

Cheon¹,

Kim²

2021

RPM

View full text Add to dashboard Cite

3D printing is an attractive method to fabricate microfluidic devices due to (1) its fast and simple process without specialized equipment and cleanroom environment, and (2) its capability to create complex 3D structures. Combined with Polydimethylsiloxane (PDMS), it can be used to develop various microfluidic devices taking advantage of both 3D printing and PDMS. In this paper, we investigated a Digital Light Processing (DLP) 3D printer to fabricate 3D printing/PDMS integrated microfluidic devices. We used it to fabricate both a master mold for the PDMS process and a substrate containing pneumatic ports and channels. The optimal design parameters to print a symmetrical microchannel structure were determined. We also measured the printing accuracy of taper structures as an example of its capability to fabricate complex structures. Then, we fabricated a microfluidic device by integrating a PDMS component with a 3D printed substrate. The microfluidic device operation was demonstrated using dye solutions. The fluidic control results clearly show the microfluidic device works as expected.

show abstract

Microbial single-cell analysis in picoliter-sized batch cultivation chambers

Cited by 26 publications

References 38 publications

microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation

microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation

Heterogeneous Microfluidic Reactors: A Review and an Insight of Enzymatic Reactions

Fabrication and Demonstration of a 3D-printing/PDMS Integrated Microfluidic Device

Contact Info

Product

Resources

About