FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data

Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories

A position- and time-sensitive photon-counting detector with delay-line read-out

We have developed image intensifier tubes with delay-anode read-out for time- and position-sensitive photon counting. The timing precision is better than 1 ns with 1000x1000 pixels position resolution and up to one megacounts/s processing rate. Large format detectors of 40 and 75 mm active diameter with internal helical-wire delay-line anodes have been produced and specified. A different type of 40 and 25 mm tubes with semi-conducting screen for image charge read-out allow for an economic and robust tube design and for placing the read-out anodes outside the sealed housing. Two types of external delay-line anodes, i.e. pick-up electrodes for the image charge, have been tested. We present tests of the detector and anode performance. Due to the low background this technique is well suited for applications with very low light intensity and especially if a precise time tagging for each photon is required. As an example we present the application of scintillator read-out in time-of-flight (TOF) neutron radiography. Further applications so far are Fluorescence Life-time Microscopy (FLIM) and AstronomyComment: Proceedings of SPIE Conference "Optics and Optoelectronics", 16 - 19. Apr.200

Instrument and data analysis challenges for imaging spectropolarimetry

The next generation of solar telescopes will enable us to resolve the fundamental scales of the solar atmosphere, i.e., the pressure scale height and the photon mean free path. High-resolution observations of small-scale structures with sizes down to 50 km require complex post-focus instruments, which employ adaptive optics (AO) and benefit from advanced image restoration techniques. The GREGOR Fabry-Perot Interferometer (GFPI) will serve as an example of such an instrument to illustrate the challenges that are to be expected in instrumentation and data analysis with the next generation of solar telescopes.Comment: 4 pages, 1 figure, accepted for publication in Astronomische Nachrichten/AN, special issue of the 1st EAST-ATST Workshop: "Science with large solar telescopes" in Freiburg, Germany, October 14-16, 200

High-repetition-rate and high-photon-flux 70 eV high-harmonic source for coincidence ion imaging of gas-phase molecules

Unraveling and controlling chemical dynamics requires techniques to image structural changes of molecules with femtosecond temporal and picometer spatial resolution. Ultrashort-pulse x-ray free-electron lasers have significantly advanced the field by enabling advanced pump-probe schemes. There is an increasing interest in using table-top photon sources enabled by high-harmonic generation of ultrashort-pulse lasers for such studies. We present a novel high-harmonic source driven by a 100 kHz fiber laser system, which delivers 10$^{11}$ photons/s in a single 1.3 eV bandwidth harmonic at 68.6 eV. The combination of record-high photon flux and high repetition rate paves the way for time-resolved studies of the dissociation dynamics of inner-shell ionized molecules in a coincidence detection scheme. First coincidence measurements on CH$_3$I are shown and it is outlined how the anticipated advancement of fiber laser technology and improved sample delivery will, in the next step, allow pump-probe studies of ultrafast molecular dynamics with table-top XUV-photon sources. These table-top sources can provide significantly higher repetition rates than the currently operating free-electron lasers and they offer very high temporal resolution due to the intrinsically small timing jitter between pump and probe pulses

J-PET Framework: Software platform for PET tomography data reconstruction and analysis

J-PET Framework is an open-source software platform for data analysis, written in C++ and based on the ROOT package. It provides a common environment for implementation of reconstruction, calibration and filtering procedures, as well as for user-level analyses of Positron Emission Tomography data. The library contains a set of building blocks that can be combined by users with even little programming experience, into chains of processing tasks through a convenient, simple and well-documented API. The generic input-output interface allows processing the data from various sources: low-level data from the tomography acquisition system or from diagnostic setups such as digital oscilloscopes, as well as high-level tomography structures e.g. sinograms or a list of lines-of-response. Moreover, the environment can be interfaced with Monte Carlo simulation packages such as GEANT and GATE, which are commonly used in the medical scientific community.Comment: 14 pages, 5 figure

Modeling of pulsed laser guide stars for the Thirty Meter Telescope project

The Thirty Meter Telescope (TMT) has been designed to include an adaptive optics system and associated laser guide star (LGS) facility to correct for the image distortion due to Earth's atmospheric turbulence and achieve diffraction-limited imaging. We have calculated the response of mesospheric sodium atoms to a pulsed laser that has been proposed for use in the LGS facility, including modeling of the atomic physics, the light-atom interactions, and the effect of the geomagnetic field and atomic collisions. This particular pulsed laser format is shown to provide comparable photon return to a continuous-wave (cw) laser of the same average power; both the cw and pulsed lasers have the potential to satisfy the TMT design requirements for photon return flux.Comment: 16 pages, 20 figure