Biology subjects

Mohanan, S.

Publications and source records attributed to Mohanan, S..

4 recordsLinked to original sources

bioRxiv2026

Random-forest segmentation and spatial analysis of injected cardiac spheroids in optically cleared myocardium

Accurate quantification of transplanted cardiac spheroids requires three-dimensional localisation within intact myocardium, yet this remains technically challenging. Optical clearing and light-sheet microscopy enable volumetric imaging of injection sites, but automated segmentation is difficult when transplanted spheroids and host tissue are labelled with the same fluorescent markers and cannot be separated by simple thresholding. We developed a random forest based pixel classification workflow for 3D detection of injected hiPSC derived cardiomyocyte and H9c2 spheroids in optically cleared rabbit myocardium. A supervised classifier trained on intensity, edge, and texture features generated a segmentation then grouped pixels via connected component analysis to reconstruct individual spheroids. The method showed good agreement with manual annotation and enabled automated extraction of spheroid size and spatial metrics. This accessible workflow enables reproducible three-dimensional quantification of transplanted spheroids in large light-sheet microscopy datasets and provides a practical route from volumetric imaging to spatial metrics in cardiac regeneration studies.

biophysics↗

bioRxiv2025

Mechanical de-skewing enables high-resolution imaging of thin tissue slices with a mesoSPIM light-sheet microscope

Optical clearing combined with light-sheet microscopy enables high-resolution imaging of extended tissue at scale. However, standard mesoSPIM systems are optimised for intact organs and are not suited to thin tissue slices. We present a no-shear imaging protocol using obliquely mounted samples held between refractive-index-matched slides in a 3D-printed frame. This enables mechanical de-skewing during acquisition, minimising post-processing requirements. We demonstrate feasibility in fluorescent bead phantoms and rabbit heart tissue, achieving a 4.8x reduction in processing time and a 1.5x improvement in axial resolution compared to the shear-method. The no-shear method extends mesoSPIMs utility to fragile, laterally extended tissue sections.

biophysics↗

bioRxiv2024

Automated measurement of cardiomyocyte monolayer contraction using the Exeter Multiscope

We apply a novel microscope architecture, the Exeter Multiscope, to the problem of acquiring image data in rapid succession from nine wells of a 96 well plate. We demonstrate that the new microscope can detect contraction in cardiomyocyte monolayers which have been plated into these wells. Each well is sampled using 500 x 500 pixels across a 1.4 x 1.4 mm field of view, acquired in three colours at 3.7 Hz per well. The use of multiple illumination wavelengths provides post-hoc focus selection, further increasing the level of automation. The performance of the Exeter Multiscope is benchmarked against industry standard methods using a commercial microscope with a motorised stage and demonstrates that the Multiscope can acquire data almost 40 times faster. The data from both Multiscope and the commercial systems are processed by a pixel variance algorithm that uses information from the pixel value variability over time to determine the timing and amplitude of tissue contraction. This algorithm is also benchmarked against an existing algorithm that employs an absolute difference measure of tissue contraction.

biophysics↗

bioRxiv2019

Solid State High Throughput Screening Microscopy

We introduce a solid state high throughput screening (ssHTS) imaging modality that uses a novel Newtonian telescope design to image multiple spatially separated samples without moving parts or robotics. Conventional high-throughput imaging modalities either require movement of the sample to the focal plane of the imaging system1-3 or movement of the imaging system itself4,5, or use a wide-field approach to capture several samples in one frame. Schemes which move the sample or the imaging system can be mechanically complex and are inherently slow, while wide-field imaging systems have poor light collection efficiency and resolution compared to systems that image a single sample at a given time point. Our proposed ssHTS system uses a large parabolic reflector and an imaging lenses positioned at their focal distances above each sample. A fast LED array sequentially illuminate samples to generate images that are captured with a single camera placed at the focal point of the reflector. This optical configuration allows each sample to completely fill a sensors field of view. Since each LED illuminates a single sample and LED switch times are very fast, images from spatially separated samples can be captured at rates limited only by the cameras frame rate. The system is demonstrated by imaging cardiac monolayer and Caenorhabditis elegans (C. elegans) preparations.

bioengineering↗