Simultaneous whole-animal 3D-imaging of neuronal activity using light field microscopy

3D functional imaging of neuronal activity in entire organisms at single cell level and physiologically relevant time scales faces major obstacles due to trade-offs between the size of the imaged volumes, and spatial and temporal resolution. Here, using light-field microscopy in combination with 3D deconvolution, we demonstrate intrinsically simultaneous volumetric functional imaging of neuronal population activity at single neuron resolution for an entire organism, the nematode Caenorhabditis elegans. The simplicity of our technique and possibility of the integration into epi-fluoresence microscopes makes it an attractive tool for high-speed volumetric calcium imaging.Comment: 25 pages, 7 figures, incl. supplementary informatio

The Hard X-Ray View of the Young Supernova Remnant G1.9+0.3

NuSTAR observed G1.9+0.3, the youngest known supernova remnant in the Milky Way, for 350 ks and detected emission up to $\sim$30 keV. The remnant's X-ray morphology does not change significantly across the energy range from 3 to 20 keV. A combined fit between NuSTAR and CHANDRA shows that the spectrum steepens with energy. The spectral shape can be well fitted with synchrotron emission from a power-law electron energy distribution with an exponential cutoff with no additional features. It can also be described by a purely phenomenological model such as a broken power-law or a power-law with an exponential cutoff, though these descriptions lack physical motivation. Using a fixed radio flux at 1 GHz of 1.17 Jy for the synchrotron model, we get a column density of N$_{\rm H}$ = $(7.23\pm0.07) \times 10^{22}$ cm$^{-2}$, a spectral index of $\alpha=0.633\pm0.003$, and a roll-off frequency of $\nu_{\rm rolloff}=(3.07\pm0.18) \times 10^{17}$ Hz. This can be explained by particle acceleration, to a maximum energy set by the finite remnant age, in a magnetic field of about 10 $\mu$G, for which our roll-off implies a maximum energy of about 100 TeV for both electrons and ions. Much higher magnetic-field strengths would produce an electron spectrum that was cut off by radiative losses, giving a much higher roll-off frequency that is independent of magnetic-field strength. In this case, ions could be accelerated to much higher energies. A search for $^{44}$Ti emission in the 67.9 keV line results in an upper limit of $1.5 \times 10^{-5}$ $\,\mathrm{ph}\,\mathrm{cm}^{-2}\,\mathrm{s}^{-1}$ assuming a line width of 4.0 keV (1 sigma).Comment: 9 pages, 6 figures, accepted Ap

Video-rate volumetric neuronal imaging using 3D targeted illumination

Fast volumetric microscopy is required to monitor large-scale neural ensembles with high spatio-temporal resolution. Widefield fluorescence microscopy can image large 2D fields of view at high resolution and speed while remaining simple and costeffective. A focal sweep add-on can further extend the capacity of widefield microscopy by enabling extended-depth-of-field (EDOF) imaging, but suffers from an inability to reject out-of-focus fluorescence background. Here, by using a digital micromirror device to target only in-focus sample features, we perform EDOF imaging with greatly enhanced contrast and signal-to-noise ratio, while reducing the light dosage delivered to the sample. Image quality is further improved by the application of a robust deconvolution algorithm. We demonstrate the advantages of our technique for in vivo calcium imaging in the mouse brain.This work was funded by the National Institutes of Health (R21EY026310) and the National Science Foundation (CBET-1508988). The authors wish to thank E. McCarthy and Prof. M.J. Baum for providing mouse brain slices used in this manuscript, and A. I. Mohammed for providing in vivo mouse brain samples in the early stages of this work. (R21EY026310 - National Institutes of Health; CBET-1508988 - National Science Foundation)Published versio

Confocal microscopy of colloidal particles: towards reliable, optimum coordinates

Over the last decade, the light microscope has become increasingly useful as a quantitative tool for studying colloidal systems. The ability to obtain particle coordinates in bulk samples from micrographs is particularly appealing. In this paper we review and extend methods for optimal image formation of colloidal samples, which is vital for particle coordinates of the highest accuracy, and for extracting the most reliable coordinates from these images. We discuss in depth the accuracy of the coordinates, which is sensitive to the details of the colloidal system and the imaging system. Moreover, this accuracy can vary between particles, particularly in dense systems. We introduce a previously unreported error estimate and use it to develop an iterative method for finding particle coordinates. This individual-particle accuracy assessment also allows comparison between particle locations obtained from different experiments. Though aimed primarily at confocal microscopy studies of colloidal systems, the methods outlined here should transfer readily to many other feature extraction problems, especially where features may overlap one another.Comment: Accepted by Advances in Colloid and Interface Scienc

Extending AMCW lidar depth-of-field using a coded aperture

By augmenting a high resolution full-field Amplitude Modulated Continuous Wave lidar system with a coded aperture, we show that depth-of-field can be extended using explicit, albeit blurred, range data to determine PSF scale. Because complex domain range-images contain explicit range information, the aperture design is unconstrained by the necessity for range determination by depth-from-defocus. The coded aperture design is shown to improve restoration quality over a circular aperture. A proof-of-concept algorithm using dynamic PSF determination and spatially variant Landweber iterations is developed and using an empirically sampled point spread function is shown to work in cases without serious multipath interference or high phase complexity