Lamb JR, Ward EN, Kaminski CF. "An open-source software package for on-the-fly deskewing and live viewing of volumetric lightsheet microscopy data" arXiv:2211.00645 (2022) DOI
Abstract: Oblique plane microscopy, OPM, is a form of lightsheet microscopy that permits volumetric imaging of biological samples at high temporal and spatial resolution. However, the imaging geometry of OPM, and related variants of light sheet microscopy, distorts the coordinate frame of the presented image sections with respect to real space coordinate frame in which the sample is moved to navigate to regions of interest. This makes live viewing and practical operation of such microscopes difficult. We present an open-source software package that utilises GPU acceleration and multiprocessing to transform the display of OPM imaging data in real time to produce live views that mimic that produced by standard widefield microscopes. Image stacks can be acquired, processed and plotted at rates of several Hz, making live operation of OPMs, and similar microscopes, more user friendly and intuitive.
Illustration of two different operational modes of the software to permit operation at either low, or fast imaging acquisition speed. For fast frame rates, global updating of the data stack is used: For slow acquisition speeds a rolling update is used. Camera exposure time is the most influential parameter on software frame rate. (a) Global mode updates the output image after every full stack. However, for long exposure times, this renders the frame rate too low for facile navigation of the sample. Rolling mode updates the output images after each raw image is received from the camera and processed. Global (b) and rolling (c) update modes are shown for the imaging of microtubules in Vero cells. The scale bar is 25um.
