The overwhelming majority of research in the neurosciences employs P-values stemming from tests of statistical significance to decide on the presence or absence of an effect of some treatment variable. Although a continuous variable, the P-value is commonly used to reach a dichotomous decision about the presence of an effect around an arbitrary criterion of 0.05. This analysis strategy is widely used, but has been heavily criticized in the past decades. To counter frequent misinterpretations of P-values, it has been advocated to complement or replace P-values with measures of effect size (MES). Many psychological, biological and medical journals now recommend reporting appropriate MES. One hindrance to the more frequent use of MES may be their scarcity in standard statistical software packages. Also, the arguably most widespread data analysis software in neuroscience, matlab, does not provide MES beyond correlation and receiver-operating characteristic analysis. Here we review the most common criticisms of significance testing and provide several examples from neuroscience where use of MES conveys insights not amenable through the use of P-values alone. We introduce an open-access matlab toolbox providing a wide range of MES to complement the frequently used types of hypothesis tests, such as t-tests and analysis of variance. The accompanying documentation provides calculation formulae, intuitive explanations and example calculations for each measure. The toolbox described is usable without sophisticated statistical knowledge and should be useful to neuroscientists wishing to enhance their repertoire of statistical reporting.

Neuronal activity has been shown to be essential for the proper formation of neuronal circuits, affecting developmental processes like neurogenesis, migration, programmed cell death, cellular differentiation, formation of local and long-range axonal connections, synaptic plasticity or myelination. Accordingly, neocortical areas reveal distinct spontaneous and sensory-driven neuronal activity patterns already at early phases of development. At embryonic stages, when immature neurons start to develop voltage-dependent channels, spontaneous activity is highly synchronized within small neuronal networks and governed by electrical synaptic transmission. Subsequently, spontaneous activity patterns become more complex, involve larger networks and propagate over several neocortical areas. The developmental shift from local to large-scale network activity is accompanied by a gradual shift from electrical to chemical synaptic transmission with an initial excitatory action of chloride-gated channels activated by GABA, glycine and taurine. Transient neuronal populations in the subplate (SP) support temporary circuits that play an important role in tuning early neocortical activity and the formation of mature neuronal networks. Thus, early spontaneous activity patterns control the formation of developing networks in sensory cortices, and disturbances of these activity patterns may lead to long-lasting neuronal deficits.

The rat whisker system has evolved into in an excellent model system for sensory processing from the periphery to cortical stages. However, to elucidate how sensory processing finally relates to percepts, methods to assess psychophysical performance pertaining to precise stimulus kinematics are needed. Here, we present a head-fixed, behaving rat preparation that allowed us to measure detectability of a single whisker deflection as a function of amplitude and peak velocity. We found that velocity thresholds for detection of smallamplitude stimuli (Ͻ3°) were considerably higher than for detection of large-amplitude stimuli (Ͼ3°). This finding suggests the existence of two psychophysical channels mediating detection of whisker deflection: one channel exhibiting high amplitude and low velocity thresholds (W1), and the other channel exhibiting high velocity and low amplitude thresholds (W2). The correspondence of W1 to slowly adapting (SA) and W2 to rapidly adapting (RA) neuronal classes in the trigeminal ganglion was revealed in acute neurophysiological experiments. Neurometric plots of SA and RA cells were closely aligned to psychophysical performance in the corresponding W1 and W2 parameter ranges. Interestingly, neurometric data of SA cells fit the behavior best if it was based on a short time window integrating action potentials during the initial phasic response, in contrast to integrating across the tonic portion of the response. This suggests that detection performance in both channels is based on the assessment of very few spikes in their corresponding groups of primary afferents.

This paper describes experimental techniques with head-fixed, operantly conditioned rodents that allow the control of stimulus presentation and tracking of motor output at hitherto unprecedented levels of spatio-temporal precision. Experimental procedures for the surgery and behavioral training are presented. We place particular emphasis on potential pitfalls using these procedures in order to assist investigators who intend to engage in this type of experiment. We argue that head-fixed rodent models, by allowing the combination of methodologies from molecular manipulations, intracellular electrophysiology, and imaging to behavioral measurements, will be instrumental in combining insights into the functional neuronal organization at different levels of observation. Provided viable behavioral methods are implemented, model systems based on rodents will be complementary to current primate models—the latter providing highest comparability with the human brain, while the former offer hugely advanced methodologies on the lower levels of organization, for example, genetic alterations, intracellular electrophysiology, and imaging.