961 Works

3D cyto- and receptor architectonic map of macaque lateral premotor area F5v

L. Rapan, S. Froudist-Walsh, M. Niu, T. Funck, K. Zilles & N. Palomero-Gallagher
A multimodal analysis of the macaque motor cortex was carried out to create a 3D atlas integrating and reconciling discrepancies between previously published maps. This involved a quantitative and statistically testable approach to the analysis of cytoarchitecture in the macaque monkey frontal agranular cortex, in combination with an in vitro quantitative receptor autoradiographic analysis of the regional and laminar distribution patterns of 13 different neurotransmitter receptors. The borders of the identified areas were traced onto...

Probabilistic cytoarchitectonic map of Area Fo5 (OFC) (v2.1)

M. Wojtasik, H. Mohlberg & K. Amunts
This dataset contains the distinct architectonic Area Fo5 (OFC) in the MNI Colin 27 and MNI ICBM 152 reference spaces. As part of the Julich-Brain atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. Subsequently the results of the cytoarchitectonic analysis are mapped to the MNI Colin 27 and MNI ICBM 152 reference spaces where each...

Cytoarchitectonic areas of human auditory cortex on individual brain surfaces

Ö. F. Gülban, R. Goebel, D. Zachlod, H. Mohlberg, K. Amunts & F. De Martino
We have analyzed post mortem MRI data (10 whole brain images) used in Julich-Brain cyto-architectonic Atlas in order to segment and reconstruct individual brain cortical surface models. The resulting surfaces are used to visualize cyto-architectonic areas on cortical surfaces. These surfaces can be reused in the future to visualize other cyto-architectonic maps acquired from the same individual brains or generate surface-based probabilistic group average atlases.

Whole-brain parcellation of the Julich-Brain Cytoarchitectonic Atlas (v2.6)

K. Amunts, H. Mohlberg, S. Bludau, S. Caspers, S. B. Eickhoff & P. Pieperhoff
This dataset contains the whole-brain parcellation of the Julich-Brain Cytoarchitectonic Atlas in the MNI ICBM 152 2009c nonlinear asymmetric reference space ([Evans et al., 2012](https://www.sciencedirect.com/science/article/pii/S1053811912000419?via%3Dihub)). The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the Julich-Brain Cytoarchitectonic Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and...

Anterograde projections of the macaque ventral midbrain

M. Zubair, S. Murris, K. Isa, H. Onoe, Y. Koshimizu, K. Kobayashi, W. Vanduffel & T. Isa
To understand the connectome of the axonal arborizations of dopaminergic midbrain neurons, we investigated the anterograde spread of highly sensitive viral tracers injected into the ventral tegmental area (VTA) and adjacent areas in three macaques. In two monkeys, injections were centered on the lateral VTA with some spread into the substantia nigra, while in one animal the injection targeted the medial VTA with partial spread into the ventromedial thalamus. Double-labeling with antibodies against transduced fluorescent...

Hippocampal place cell recordings in a Four-Room navigation task

E. Duvelle, R. Grieves, A. Liu, S. Jedidi-Ayoub, J. Holeniewska, A. Harris, N. Nyberg, F. Donnarumma, J. M. Lefort, K. Jeffery, C. Summerfield, G. Pezzulo & H. Spiers
Hippocampal place cells show location-specific firing and are thought to be an essential component of the brain’s “cognitive map”, supporting flexible memorization of places and possibly of their connectivity. So far, only a few studies investigated whether these cells encode the connectivity between places, either by adding a barrier or removing a wall. We aimed to go one step further and investigated whether place cells can encode pure connectivity, i.e. changes in the “closed” or...

3D cyto- and receptor architectonic map of macaque area PFop of the inferior parietal lobe

M. Niu, L. Rapan, T. Funck, S. Froudist-Walsh, L. Zhao, K. Zilles & N. Palomero-Gallagher
A multimodal analysis of the macaque inferior parietal lobule was carried out to create a 3D atlas integrating and reconciling discrepancies between previously published maps. This involved a quantitative and statistically testable approach to the analysis of cytoarchitecture in the macaque monkey inferior parietal lobe, in combination with an in vitro quantitative receptor autoradiographic analysis of the regional and laminar distribution patterns of 15 different neurotransmitter receptors. The borders of the identified areas were traced...

3D cyto- and receptor architectonic map of macaque area PFG of the inferior parietal lobe

M. Niu, L. Rapan, T. Funck, S. Froudist-Walsh, L. Zhao, K. Zilles & N. Palomero-Gallagher
A multimodal analysis of the macaque inferior parietal lobule was carried out to create a 3D atlas integrating and reconciling discrepancies between previously published maps. This involved a quantitative and statistically testable approach to the analysis of cytoarchitecture in the macaque monkey inferior parietal lobe, in combination with an in vitro quantitative receptor autoradiographic analysis of the regional and laminar distribution patterns of 15 different neurotransmitter receptors. The borders of the identified areas were traced...

3D high resolution SRXTM image data of cortical vasculature of rat brain.

B. Weber & M. Schneider
The goal of the study is to produce the first high resolution, 3D reconstruction of the entire macrostructure and vascular system of the rat/mouse brain. To that end synchrotron radiation-based X-ray microscopy images were collected. Then the data is translated into 3D mesh and volumetric models (graph). This dataset contains high resolution tiff image array of part of cortical vasculature of the rat brain. This dataset is used as an input to computational methods that...

Ultrahigh resolution 3D cytoarchitectonic map of Area hOc3v (LingG) created by a Deep-Learning assisted workflow

C. Schiffer, K. Kiwitz, K. Amunts & T. Dickscheid
This dataset contains automatically created cytoarchitectonic maps of Area hOc3v (LingG) in the BigBrain. Mappings were created using Deep Convolutional Neural networks trained on delineations on every 60th section using multivariate statistical image analysis, applied to GLI-images of coronal histological sections of 1 micron resolution. Resulting mappings are available on every section. Maps were transformed to the 3D reconstructed BigBrain space. Individual sections were used to assemble a 3D volume of the area, low quality...

Reference delineations of Area hOc3v (LingG) in individual sections of the BigBrain

K. Kiwitz, C. Schiffer, T. Dickscheid & K. Amunts
This dataset contains cytoarchitectonic maps of area hOc3v (LingG) in the BigBrain. The mappings were created using multivariate statistical image analysis, applied to GLI-images of coronal histological sections of 1 micron resolution. Mappings are available on 38 sections of the occipital lobe of the BigBrain and have been transformed to the 3D reconstructed BigBrain space. For this brain area, a highly detailed 3D map has been computed based on automatic delineations on every histological section...

Genetic variants in autistic and typically developing individuals

C. Leblond, F. Cliquet, A. Mathieu, R. Delorme & T. Bourgeron
The main goal was to analyze the relationship between genotype and phenotype for individuals carrying synaptic mutations. Thus, we extracted from the PARIS cohort individuals (175 autistic individuals and 128 typically developing) all the impactful mutations that are synaptic or directly associated with autism.

Human ultra-high resolution functional imaging data (7 Tesla) on multi-element event memories (general raw data)

X. Grande, D. Berron, A. J. Horner, J. A. Bisby, E. Düzel & N. Burgess
Ultra-high resolution 7Tesla functional MRI data (0.8 mm isotropic) was acquired in 30 young, healthy adults. During data acquisition, participants performed the encoding and retrieval phase of a memory task. Participants learned events, consisting of a popular person, an object (or animal) and a location in a pairwise associative manner. At retrieval, in a 4-alternative forced choice recognition task, one event element served as a cue while a belonging target element was presented among familiar...

3D ultrastructural study of synapses using FIB/SEM in the human Entorhinal Cortex

L. Alonso-Nanclares, M. Dominguez-Alvaro, L. Blazquez-Llorca, M. Montero-Crespo & J. DeFelipe
We used Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) to perform a three-dimensional analysis of the synapses in the neuropil in different layers of the medial Entorhinal Cortex (EC) from human brain autopsies. Specifically, we studied synaptic structural parameters of synapses, which were fully reconstructed in 3D. We analyzed the synaptic density, 3D spatial distribution, and type (excitatory and inhibitory), as well as the shape and size of each synaptic junction. Moreover, the postsynaptic targets of...

Layer-specific excitatory and inhibitory neuronal maps of hippocampus (v1.1)

I. Costantini, G. Mazzamuto, L. Pesce, V. Gavryusev, A. Laurino, M. Scardigli & F. Pavone
The aim of this work is to reconstruct the 3D organization of neurons in a left hippocampus from sub-cellular resolution images obtained by a custom-made dual view inverted light sheet fluorescence microscope. We analyze the left hippocampus of a 99-year old woman, not affected by Alzheimer’s disease, nor hypertension, but presenting a cognitive decline, obtained from the University of Tours. The sample was cut into 72 slices of 500 um thickness before imaging. Each slice...

Molecular characterization of the interneurons in human temporal neocortex by two photon fluorescence microscopy (v1.1)

I. Costantini, G. Mazzamuto, L. Pesce, M. Scardigli & F. Pavone
The aim of this work is to study the 3D organization of some population of interneurons within a sample of interest, previously analyzed for physiological information, using two photon fluorescence microscopy (TPFM). We exploit the high axial and radial resolution of TPFM optical sectioning (0.44 x 0.44 x 2 μm³) in combination with a protocol for tissue clearing and labeling to perform the 3D reconstruction of 300 um thick brain sections. We clear the sections...

Molecular characterization of the interneurons in human temporal neocortex by two photon fluorescence microscopy (v1.0)

I. Costantini & G. Mazzamuto
The aim of this work is to study the 3D organization of some population of interneurons within a sample of interest, previously analyzed for physiological information, using two photon fluorescence microscopy (TPFM). We exploit the high axial and radial resolution of TPFM optical sectioning (0.44 x 0.44 x 2 μm³) in combination with a protocol for tissue clearing and labeling to perform the 3D reconstruction of 300 um thick brain sections. We clear the sections...

Regional and laminar distribution of silver stained cell bodies in the rat brain

L. Zhao, K. Zilles & N. Palomero-Gallagher
Classical mapping studies relied on the analysis of histologically processed sections from formalin-fixed brains for the identification of borders between cortical areas or of the boundaries of subcortical nuclei. Differences in the regional and laminar distribution patterns of neurotransmitter receptors are known to complement and extend the insights into the structural organization of the brain, which are provided by cytoarchitectonic observations alone. Since the method of quantitative *in vitro* receptor autoradiography requires processing of unfixed,...

Dose-dependent effects of ketamine on spontaneous and evoked EEG activity in rats

A. Arena, S. Thon & J. Storm
This dataset contains recordings of spontaneous epidural EEG from a large number of cortical areas and evoked related potentials (ERPs) following local electrical cortical stimulation in 6 rats during deep ketamine anesthesia (keta2). These data can be used in combination with the EBRAINS dataset [PCI-like measure in rodents](https://doi.org/10.25493/S0DM-BK5), where the same rats were recorded during wakefulness (wake) and light ketamine anesthesia (keta1), to identify dose dependent effects of ketamine in cortical activity. For subject j07,...

Regional and laminar distribution of receptors for acetylcholine in the rat brain

L. Zhao, K. Zilles & N. Palomero-Gallagher
The present dataset provides the quantitative regional and laminar distribution of key molecules in signal transfer, namely the muscarinic acetylcholine M1, M2 and M3 receptors as well as the nicotinic acetylcholine α4β2 receptor, in five selected rostrocaudal levels of the rat brain. The receptors were visualized by means of quantitative *in vitro* receptor autoradiography and the selective tritiated ligands pirenzepine, oxotremorine-M, 4-DAMP and epibatidine. The high spatial resolution of this method enables quantification of receptor...

Cortical activity features in transgenic mouse models of cognitive deficits (Williams Beuren Syndrome)

M. Sanchez-Vives
High-density electrocorticogram recordings were performed in the cerebral cortex of ketamine-medetomidine anaesthetized adult wild-type and knock out mice to characterize the dynamics of emergent slow oscillatory activity. A new analysis pipeline has been refined and improved by enrichment with novel methods and functions accounting for the fine spatial and temporal resolution of the data. The combination of high-density electrode recordings with a detailed analytical tool allows the establishment of an unprecedented correlation of slow wave...

Large scale multi-channel EEG in rats

A. Arena & J. Storm
The aim of this task is to develop a protocol and a set-up for recording EEG signal from a large number of cortical areas in head-restrained rats exposed to anesthesia and during wakefulness. In order to quantify cortical complexity and its relation to (un)consciousness, a large scale EEG that samples activity from most of cortical areas is needed (Massimini et al. Science, 2005; Casali et al. Sci Transl Med, 2013). Unfortunately, only few existing probes...

Maps of neurons stained with anti-NeuN antibody

F. Pavone & I. Costantini
This dataset is about 3D-imaging at high resolution of NeuN expressing neurons of selected regions (area 17 of visual cortex) of human brain. The dataset contains the final fused volume in tiff and MP4 format, the originally acquired 3D stacks, as well as the stitching file generated by ZetaStitcher.

Purkinje cell protein 2 tetracycline-transactivator expression: horizontal sections (case 3292)

S. Lillehaug, M. Yetman, M. Puchades, M. Checinska, J. Jankowsky, J.G. Bjaalie & T.B. Leergaard
Bright-field microscopy images of serial horizontal brain sections showing Purkinje cell protein 2 (Pcp2) promoter expression in a bigenic Pcp2-tetracycline-transactivator (tTA) mouse brain (case 3292, adult female), generated using a driver-reporter construct in which the PCP2-tTA promoter regulates the expression of the E. coli derived LacZ reporter gene encoding β-galactosidase, which is visualized histologically using X-gal (5-Bromo-4-chloro-3-indolyl β-d-galactopyranoside) as a substrate. Our data confirm earlier reports that Pcp2-tTA promoter expression is restricted to cerebellar Purkinje...

Pituitary homeobox 3 tetracycline-transactivator expression: coronal sections (case 6517)

S. Lillehaug, M. Yetman, M. Puchades, M. Checinska, J. Jankowsky, J.G. Bjaalie & T.B. Leergaard
Bright-field microscopy images of serial coronal brain sections showing Pituitary homeobox 3 (Pitx3) promoter expression in a bigenic Pitx3-tetracycline-transactivator (tTA) mouse brain (case 6517, adult female), using a driver-reporter construct in which the Pitx3-tTA promoter regulates the expression of the E. coli derived LacZ reporter gene encoding β-galactosidase, which is visualized histologically using X-gal (5-Bromo-4-chloro-3-indolyl β-d-galactopyranoside) as a substrate. Our data show that the Pitx3-tTA promoter is spatially restricted to the substantia nigra, ventral tegmental...

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