A standardized and reproducible method to measure decision-making in mice.

Abstract Progress in neuroscience is hindered by poor reproducibility of mouse behavior. Here we show that in a visual decision making task, reproducibility can be achieved by automating the training protocol and by standardizing experimental hardware, software, and procedures. We trained 101 mice in this task across seven laboratories at six different research institutions in three countries, and obtained 3 million mouse choices. In trained mice, variability in behavior between labs was indistinguishable from variability within labs. Psychometric curves showed no significant differences in visual threshold, bias, or lapse rates across labs. Moreover, mice across laboratories adopted similar strategies when stimulus location had asymmetrical probability that changed over time. We provide detailed instructions and open-source tools to set up and implement our method in other laboratories. These results establish a new standard for reproducibility of rodent behavior and provide accessible tools for the study of decision making in mice

Tonotopic organization in monkey and human auditory cortex using phase-encoded functional MRI

Tonotopic organization is the main topographic feature of the primary auditory cortex. Importantly, tonotopy allows to define borders of cortical areas as reversals of the frequency gradient (i.e the spatial derivative of the preferred frequency map). Very different tonotopic organisations have been described with respect to Heschl’s gyrus in humans. Furthermore, human tonotopy remains difficult to relate to the organization in nonhuman primates and a comparison would require the same measurement, design and analysis in both species. Here, we measured blood oxygen leveldependent signal with functional MRI (fMRI) in humans and monkeys. We applied phase-encoded designs ('travelling wave') and performed surface-based analyses using high-resolution individual anatomical MRIs. Thirteen humans and three rhesus monkeys were scanned during passive listening. Monkeys were scanned at 4.7 Tesla and humans were scanned at 3T and 7T. Two run types with either low-to-high or high-to-low progression of tone bursts were alternated. Crosscorrelation between time-series from both run types were computed and time delay between the two signals revealed the preferred frequency. In monkeys, we found a tonotopic pattern with a posteroanterior axis of high-low-high preference located at the coordinates of A1-R according to monkey atlas. In humans, we also observed a tonotopic pattern of high-low-high preference along an overall postero-anterior axis, running across Heschl’s gyrus. Our findings suggest that the precise 3D representation of the individual cortical surface is critical to better appreciate the organization in both species. This first comparative fMRI study of the tonotopy would contribute to the definition of a unified primate model of core and belt fields (Baumann et al., 2013)

CONSTRUCTION A POSTERIORI DU PEDIGREE D'UNE POPULATION EXPERIMENTALE DE CANARDS A L'AIDE D'OUTILS MOLECULAIRES

With the 2010/63/UE directive coming into force, the INRAE experimental facilities dealing with waterfowl had to imagine a new scheme in order to produce cohorts of offspring of known pedigree in three populations of ducks without resorting to cages for layers. A set of 96 SNP markers was therefore used to obtain pedigree knowledge through parentage assignment. In each parental population, roughly 96 dams were dispatched in 3 cells. Within each cell, they were split into 3 or 4 groups, and were inseminated using a mixed pool of semen from 3 to 4 drakes. The hierarchical mating design commonly used in poultry breeding was therefore replaced with a factorial design. In order to avoid tricky situations in the parentage assignment, such as a difficulty to find which of two brothers is the true sire (conversely which of two sisters is the true dam), groups of parents were built so that no sibs were pooled together. Despite the limited number of markers, assignment success was very high (above 96%) for common and mule offspring. Missing parents led to a reduced success rate (88%) for Muscovy offspring. Therefore, this set of markers offers a possible alternative to individual cages, including in breeding companies which are concerned by the forthcoming EU ban of cages, provided the availability of a tool allowing for the control of laying performances of females.L’entrée en vigueur de la directive 2010/63/UE relative à la protection des animaux utilisés à des fins scientifiques a conduit l’Unité Expérimentale des Palmipèdes à Foie Gras (INRAE) à reconsidérer la conduite de ses lignées nécessitant la connaissance du pedigree. Pour connaitre la généalogie de 3 populations de canards (Pékin, Barbarie et leur hybride mulard) dans un programme expérimental en cours, il s’agissait de concevoir un plan d’accouplement au sol (sans recourir aux cages individuelles pour les femelles) compatible avec l’utilisation d’un panel de 96 marqueurs SNP développé parallèlement. Dans chaque cellule (3 par population parentale) environ 32 femelles étaient réparties en 4 groupes de 8 pour les canes de Barbarie ou 3 groupes de 11 pour les canes Pékin. Chacun de de ces groupes était inséminé par la semence mélangée d’un pool de 4 mâles. On a donc remplacé un schéma hiérarchique classique en volailles (1 ♂ et k ♀) par un schéma factoriel (p ♂ et q ♀) habituellement rencontré en aquaculture. Les groupes de reproducteurs étaient constitués de façon à faciliter l’assignation, c’est-à-dire en évitant de rassembler des frères ou des sœurs au sein du même groupe. La consanguinité attendue a également été limitée en évitant les pères communs entre groupes de ♂ et de ♀ associés. Malgré la taille réduite du panel (96 marqueurs), son pouvoir d’assignation et la connaissance du plan d’accouplement et de la cellule où l’œuf a été ramassé ont permis la réassignation à un couple unique pour plus de 96% des individus en mulards et Pékin. Pour les Barbarie, l’absence d’une dizaine de génotypes parentaux a fait chuter ce succès à 88%. Sous réserve de pouvoir contrôler la ponte, ce type de panel concourt, pour un coût limité, à la mise en œuvre d’alternatives à la cage individuelle en sélectio

A modular architecture for organizing, processing and sharing neurophysiology data

We describe an architecture for organizing, integrating and sharing neurophysiology data within a single laboratory or across a group of collaborators. It comprises a database linking data files to metadata and electronic laboratory notes; a module collecting data from multiple laboratories into one location; a protocol for searching and sharing data and a module for automatic analyses that populates a website. These modules can be used together or individually, by single laboratories or worldwide collaborations

A modular architecture for organizing, processing and sharing neurophysiology data

We describe an architecture for organizing, integrating and sharing neurophysiology data within a single laboratory or across a group of collaborators. It comprises a database linking data files to metadata and electronic laboratory notes; a module collecting data from multiple laboratories into one location; a protocol for searching and sharing data and a module for automatic analyses that populates a website. These modules can be used together or individually, by single laboratories or worldwide collaborations

Standardized and reproducible measurement of decision-making in mice.

Progress in science requires standardized assays whose results can be readily shared, compared, and reproduced across laboratories. Reproducibility, however, has been a concern in neuroscience, particularly for measurements of mouse behavior. Here, we show that a standardized task to probe decision-making in mice produces reproducible results across multiple laboratories. We adopted a task for head-fixed mice that assays perceptual and value-based decision making, and we standardized training protocol and experimental hardware, software, and procedures. We trained 140 mice across seven laboratories in three countries, and we collected 5 million mouse choices into a publicly available database. Learning speed was variable across mice and laboratories, but once training was complete there were no significant differences in behavior across laboratories. Mice in different laboratories adopted similar reliance on visual stimuli, on past successes and failures, and on estimates of stimulus prior probability to guide their choices. These results reveal that a complex mouse behavior can be reproduced across multiple laboratories. They establish a standard for reproducible rodent behavior, and provide an unprecedented dataset and open-access tools to study decision-making in mice. More generally, they indicate a path toward achieving reproducibility in neuroscience through collaborative open-science approaches