Biology subjects

Alexandrov, Y.

Publications and source records attributed to Alexandrov, Y..

4 recordsLinked to original sources

bioRxiv2022

Robust, single-shot, optical autofocus system utilizing cylindrical lenses to provide high precision and long range of operation

We present a robust, "real-time" optical autofocus system for microscopy that provides high accuracy (<230 nm) and long range ([~]130 {micro}m) with a 1.4 numerical aperture oil immersion objective lens. This autofocus can operate in a closed loop, single-shot functionality over a range of {+/-}37.5 {micro}m and can also operate as a 2-step process up to {+/-}68 {micro}m. A real-time autofocus capability is useful for experiments with long image data acquisition times, including single molecule localization microscopy, that may be impacted by defocusing resulting from drift of components, e.g., due to changes in temperature or mechanical drift. It is also vital for automated slide scanning or multiwell plate imaging where the sample may not be in the same horizontal plane for every field of view during the image data acquisition. To realise high precision and long range, we implement orthogonal optical readouts using cylindrical lenses. We demonstrate the performance of this new optical autofocus system with automated multiwell plate imaging and single molecule localisation microscopy and illustrate the benefit of using a superluminescent diode as the autofocus light source.

bioengineering↗

bioRxiv2021

Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast

We present a robust, low-cost single-shot implementation of differential phase microscopy utilising a polarisation-sensitive camera to simultaneously acquire 4 images from which the phase gradients and quantitative phase image can be calculated. This polarisation-resolved differential phase contrast (pDPC) microscopy technique can be interleaved with single-shot imaging polarimetry.

biophysics↗

bioRxiv2021

Robust optical autofocus system utilizing neural networks trained for extended range and time-course and automated multiwell plate imaging including single molecule localization microscopy

We present a robust, long-range optical autofocus system for microscopy utilizing machine learning. This can be useful for experiments with long image data acquisition times that may be impacted by defocusing resulting from drift of components, e.g. due to changes in temperature or mechanical drift. It is also useful for automated slide scanning or multiwell plate imaging where the sample(s) to be imaged may not be in the same horizontal plane throughout the image data acquisition. To address the impact of (thermal or mechanical) fluctuations over time in the optical autofocus system itself, we utilise a convolutional neural network (CNN) that is trained over multiple days to account for such fluctuations. To address the trade-off between axial precision and range of the autofocus, we implement orthogonal optical readouts with separate CNN training data, thereby achieving an accuracy well within the 600 nm depth of field of our 1.3 numerical aperture objective lens over a defocus range of up to approximately +/- 100 m. We characterise the performance of this autofocus system and demonstrate its application to automated multiwell plate single molecule localisation microscopy.

bioengineering↗

bioRxiv2018

Modelling mitosis with multiple phenotypes: relation to Haeckels biogenetic recapitulation law

The article presents a novel stochastic mathematical model of mitosis in heterogeneous (multiple-phenotype), age-dependent cell populations. The developed computational techniques involve flexible use of differentiation tree diagrams. The applicability of the model is discussed in the context of the Haeckelian (biogenetic) paradigm. In particular, the article puts forward the conjecture of generality of Haeckels recapitulation law. The conjecture is briefly collated against relevant scientific evidence and elaborated for the specific case of evolving/mutable cell phenotypes as considered by the model. The feasibility, basic regimes and the convenience of the model are tested on examples and experimental data, and the corresponding open source simulation software is described and demonstrated.

physiology↗