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

Implicit cognition is impaired and dissociable in a head-injured group with executive deficits

Implicit or non-conscious cognition is traditionally assumed to be robust to pathology but Gomez-Beldarrain et al (1999, 2002) recently showed deficits on a single implicit task after head injury. Laboratory research suggests that implicit processes dissociate. This study therefore examined implicit cognition in 20 head-injured patients and age- and I.Q.-matched controls using a battery of four implicit cognition tasks: a Serial Reaction Time task (SRT), mere exposure effect task, automatic stereotype activation and hidden co-variation detection. Patients were assessed on an extensive neuropsychological battery, and MRI scanned. Inclusion criteria included impairment on at least one measure of executive function. The patient group was impaired relative to the control group on all the implicit cognition tasks except automatic stereotype activation. Effect size analyses using the control mean and standard deviation for reference showed further dissociations across patients and across implicit tasks. Patients impaired on implicit tasks had more cognitive deficits overall than those unimpaired, and a larger Dysexecutive Self/Other discrepancy (DEX) score suggesting greater behavioural problems. Performance on the SRT task correlated with a composite measure of executive function. Head-injury thus produced heterogeneous impairments in the implicit acquisition of new information. Implicit activation of existing knowledge structures appeared intact. Impairments in implicit cognition and executive function may interact to produce dysfunctional behaviour after head-injury. Future comparisons of implicit and explicit cognition should use several measures of each function, to ensure that they measure the latent variable of interest

DFT and BIST of a multichip module for high-energy physics experiments

Engineers at Politecnico di Torino designed a multichip module for high-energy physics experiments conducted on the Large Hadron Collider. An array of these MCMs handles multichannel data acquisition and signal processing. Testing the MCM from board to die level required a combination of DFT strategie

Children's computation of complex linguistic forms: a study of frequency and imageability effects.

This study investigates the storage vs. composition of inflected forms in typically-developing children. Children aged 8-12 were tested on the production of regular and irregular past-tense forms. Storage (vs. composition) was examined by probing for past-tense frequency effects and imageability effects--both of which are diagnostic tests for storage--while controlling for a number of confounding factors. We also examined sex as a factor. Irregular inflected forms, which must depend on stored representations, always showed evidence of storage (frequency and/or imageability effects), not only across all children, but also separately in both sexes. In contrast, for regular forms, which could be either stored or composed, only girls showed evidence of storage. This pattern is similar to that found in previously-acquired adult data from the same task, with the notable exception that development affects which factors influence the storage of regulars in females: imageability plays a larger role in girls, and frequency in women. Overall, the results suggest that irregular inflected forms are always stored (in children and adults, and in both sexes), whereas regulars can be either composed or stored, with their storage a function of various item- and subject-level factors

An eye movement corpus study of the age-of-acquisition effect

In the present study, we investigated the effects of word-level age of acquisition (AoA) on natural reading. Previous studies, using multiple language modalities, showed that earlier-learned words are recognized, read, spoken, and responded to faster than words learned later in life. Until now, in visual word recognition the experimental materials were limited to single-word or sentence studies. We analyzed the data of the Ghent Eye-tracking Corpus (GECO; Cop, Dirix, Drieghe, & Duyck, in press), an eyetracking corpus of participants reading an entire novel, resulting in the first eye movement megastudy of AoA effects in natural reading. We found that the ages at which specific words were learned indeed influenced reading times, above other important (correlated) lexical variables, such as word frequency and length. Shorter fixations for earlier-learned words were consistently found throughout the reading process, in both early (single-fixation durations, first-fixation durations, gaze durations) and late (total reading times) measures. Implications for theoretical accounts of AoA effects and eye movements are discussed

Data acquisition system for the MuLan muon lifetime experiment

We describe the data acquisition system for the MuLan muon lifetime experiment at Paul Scherrer Institute. The system was designed to record muon decays at rates up to 1 MHz and acquire data at rates up to 60 MB/sec. The system employed a parallel network of dual-processor machines and repeating acquisition cycles of deadtime-free time segments in order to reach the design goals. The system incorporated a versatile scheme for control and diagnostics and a custom web interface for monitoring experimental conditions.Comment: 19 pages, 8 figures, submitted to Nuclear Instruments and Methods