A modular software framework for the design and implementation of ptychography algorithms.

Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware programming constructs to speed up the reconstruction. In this article, we present SciComPty, a new ptychography software framework aiming at simulating ptychography datasets and testing state-of-the-art and new reconstruction algorithms. Despite its simplicity, the software leverages GPU accelerated processing through the PyTorch CUDA interface. This is essential for designing new methods that can readily be employed. As an example, we present an improved position refinement method based on Adam and a new version of the rPIE algorithm, adapted for partial coherence setups. Results are shown on both synthetic and real datasets. The software is released as open-source.

Spatial reorientation with a geometric array of auditory cues.

A visuocentric bias has dominated the literature on spatial navigation and reorientation. Studies on visually accessed environments indicate that, during reorientation, human and non-human animals encode the geometric shape of the environment, even if this information is unnecessary and insufficient for the task. In an attempt to extend our limited knowledge on the similarities and differences between visual and non-visual navigation, here we examined whether the same phenomenon would be observed during auditory-guided reorientation. Provided with a rectangular array of four distinct auditory landmarks, blindfolded, sighted participants had to learn the location of a target object situated on a panel of an octagonal arena. Subsequent test trials were administered to understand how the task was acquired. Crucially, in a condition in which the auditory cues were indistinguishable (same sound sample), participants could still identify the correct target location, suggesting that the rectangular array of auditory landmarks was encoded as a geometric configuration. This is the first evidence of incidental encoding of geometric information with auditory cues and, consistent with the theory of functional equivalence, it supports the generalisation of mechanisms of spatial learning across encoding modalities.

SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows.

When considering the acquisition of experimental synchrotron radiation (SR) X-ray CT data, the reconstruction workflow cannot be limited to the essential computational steps of flat fielding and filtered back projection (FBP). More refined image processing is often required, usually to compensate artifacts and enhance the quality of the reconstructed images. In principle, it would be desirable to optimize the reconstruction workflow at the facility during the experiment (beamtime). However, several practical factors affect the image reconstruction part of the experiment and users are likely to conclude the beamtime with sub-optimal reconstructed images. Through an example of application, this article presents SYRMEP Tomo Project (STP), an open-source software tool conceived to let users design custom CT reconstruction workflows. STP has been designed for post-beamtime (off-line use) and for a new reconstruction of past archived data at user's home institution where simple computing resources are available. Releases of the software can be downloaded at the Elettra Scientific Computing group GitHub repository https://github.com/ElettraSciComp/STP-Gui.

Enactive cinema paves way for understanding complex real-time social interaction in neuroimaging experiments.

We outline general theoretical and practical implications of what we promote as enactive cinema for the neuroscientific study of online socio-emotional interaction. In a real-time functional magnetic resonance imaging (rt-fMRI) setting, participants are immersed in cinematic experiences that simulate social situations. While viewing, their physiological reactions-including brain responses-are tracked, representing implicit and unconscious experiences of the on-going social situations. These reactions, in turn, are analyzed in real-time and fed back to modify the cinematic sequences they are viewing while being scanned. Due to the engaging cinematic content, the proposed setting focuses on living-by in terms of shared psycho-physiological epiphenomena of experience rather than active coping in terms of goal-oriented motor actions. It constitutes a means to parametrically modify stimuli that depict social situations and their broader environmental contexts. As an alternative to studying the variation of brain responses as a function of a priori fixed stimuli, this method can be applied to survey the range of stimuli that evoke similar responses across participants at particular brain regions of interest.