Ultrafast 3D fluorescence imaging via 2D-3D volume reconstruction
Supervisor: Dr Daniel Olesker
School: Physics and Astronomy
Description:
3D fluorescence imaging is conventionally performed via well-established techniques such as confocal microscopy (for highest-resolution, optically sectioned imaging), light-sheet microscopy (for faster and more gentle 3D imaging), or 2-photon imaging (for imaging deeper into scattering tissue). All these techniques require scanning of either the laser illumination and/or the sample to acquire 3D images. While this is fine for applications studying static or fixed samples where there is no risk of motion blur corrupting imaging, their application to live samples is generally limited to only those exhibiting slow dynamics that do not exceed the temporal resolution provided by these imaging modalities.
Many biological phenomena, however, occur over far shorter timescales. One pertinent example is the beating embryonic zebrafish heart, which is of significant biological interest for reasons including its regenerative capacity, genetic tractability and relevance to human cardiac health. The embryonic zebrafish is optically transparent which make it well-suited for probing with optical microscopy. However, the heart beats approximately twice every second and exhibits a complex 3D motion profile, meaning it is not possible to image using the conventional approaches mentioned above because of their limited temporal resolution. For such applications, a scan-free 3D approach that can image an entire volume at a single timepoint is required.
While such imaging is technically possible, it currently requires a significant compromise in spatial resolution. Our research group has recently developed imaging approaches that overcome this limitation, providing high-resolution snapshot 3D imaging by performing volume-reconstruction from 2D snapshot projections acquired simultaneously from different angles. We have demonstrated this workflow in simulation and constructed a microscope designed to perform such imaging. The goal of this project is to use this microscope to (i) acquire data, using a variety of samples, to demonstrate the workflow, and (ii) develop new and existing software-based volume-reconstruction pipelines to experimentally demonstrate the snapshot volumetric imaging method. Combining both elements will facilitate 4D fluorescence imaging with a temporal resolution limited only by the framerate of the camera used for imaging. This will represent a significant step forward in the application of fluorescence imaging tools to study highly dynamic scenes.
This project has both computational and practical components. The ideal candidate should ideally have some experience with image processing using python. For more information about the project please contact daniel.olesker@glasgow.ac.uk.