Automated imaging of duckweed growth and development

Duckweeds are some of the smallest angiosperms, possessing a simple body architecture and high rates of biomass accumulation. They can grow near-exponentially via clonal propagation. Understanding their reproductive biology, growth, and development is essential to unlock their potential for phytoremediation, carbon capture, and nutrition. However, there is a lack of non-laborious and convenient methods for spatially and temporally imaging an array of duckweed plants and growth conditions in the same experiment. We developed an automated microscopy approach to record time-lapse images of duckweed plants growing in 12-well cell culture plates. As a proof-of-concept experiment, we grew duckweed on semi-solid media with and without sucrose and monitored its effect on their growth over 3 days. Using the PlantCV toolkit, we quantified the thallus area of individual plantlets over time, and showed that L. minor grown on sucrose had an average growth rate four times higher than without sucrose. This method will serve as a blueprint to perform automated high-throughput growth assays for studying the development patterns of duckweeds from different species, genotypes, and conditions.

Automated parasitological diagnosis in clinical microbiology laboratories

Although there is a low prevalence of parasitological infections in Europe, the diagnosis of intestinal parasites is still difficult and laborious for microbiology laboratories. Currently, antigen detection assays and molecular biology allow a more accurate diagnosis, but these techniques have limitations as they cannot detect all the possible parasites present in the samples. The objective of the study was to evaluate the accuracy and the usefulness of automated microscopy SediMAX2 (77 Elektronika, Budapest, Hungary) in the detection of parasitic infections from feces. A total of 197 formol-fixed stool samples were processed in parallel by wet mount examination and by SediMAX2. Sensitivities, specificities and predictive values were analyzed, reaching a sensitivity of 89.51% and a specificity of 98.15% and a very good positive predictive value (99.22%). SediMAX2 is a good tool for a reliable diagnosis of intestinal parasitic infections. The rapid processing and the flexibilty of storage of images analyzed make its incorporation into the day to day laboratory routine recommendable.

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based GUI environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near-instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses “Python-Microscope” (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging.HighlightsUser-friendly setup and use for simple to complex bespoke microscopes.Facilitates collaborations between biomedical scientists and microscope technologists.Touchscreen for near-instantaneous navigation of specimen landscape.Uses Python-Microscope, for abstracted open source hardware device control.Well-suited for user training of AI-algorithms for automated microscopy.

Detection of Intestinal Parasites With Automated Sedimax2®. A New Step in the Parasitological Diagnosis in High Throughput Laboratories.

Despite the low prevalence of parasitic infections in Europe, the diagnosis of intestinal parasites is difficult and laborious for microbiology laboratories. Currently, the antigens detection kits and the molecular biology have allowed an easier diagnosis. But these techniques have also limitations due to the fact that they do not detect all possible parasites presents in the samples. The objective of the study was to evaluate the accuracy and the usefulness of SediMAX2® (77 Elektronika, Budapest, Hungary) automated microscopy in the detection of parasitic structures from feces. A total of 197 formol-fixed stool samples were processed in parallel with wet mount examination and by SediMAX2®. Sensitivities, specificities and predictive values were analyzed, reaching sensitivity of 89.51% and specificity of 98.15%. Predictive values were also calculated with a very good positive predictive value (99.22%). SediMAX2® is a good tool for a reliable diagnosis of intestinal parasitic infections. The easiness of use, processing and the flexibility in the images analyse allows its incorporation in the day to day laboratory work as an extra step for the parasitologists workload.

A High-content Screening Assay based on Automated Microscopy for Monitoring Antibiotic Susceptibility of Mycobacterium Tuberculosis Phenotypes

Background Assays enabling efficient high throughput drug screening are necessary for the discovery of new anti-mycobacterial drugs. The purpose of our work was to develop and validate an assay based on live-cell imaging which can monitor growth of two distinct phenotypes of Mycobacterium tuberculosis and to test their susceptibility to commonly used TB drugs. Results Both planktonic and cording phenotypes were successfully monitored as fluorescent objects using the live-cell imaging system Incucyte S3, allowing collection of data describing distinct characteristics of aggregate size and growth. The quantification of changes in total area of aggregates was used to define IC50 and MIC values of selected TB drugs which revealed that the cording phenotype grew more rapidly and displayed a higher susceptibility to rifampicin. A checkerboard approach, testing pair-wise combinations of sub-inhibitory concentrations of drugs, revealed rifampicin, linezolid and pretomanid as superior in inhibiting growth of cording phenotype. Conclusion Our results emphasize the efficiency of using automated live-cell imaging and its potential in high-through put whole-cell screening to evaluate existing and search for novel antimycobacterial drugs.