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opencc-zeroJan 2024View details →

Data from: Whole-brain spatial organization of hippocampal single-neuron projectomes

Mapping hippocampal single-neuron projections is essential for understanding brain-wide circuit organization and diverse functions of the hippocampus, a brain structure underlying episodic memory and cognition. Here, we reconstructed 10,100 single-neuron projectomes of the mouse hippocampus, identified rostral and caudal axon pathways that preferentially innervated cortical vs. subcortical areas, and classified 43 projectome subtypes with distinct axon targeting patterns. Notably, the soma locations along hippocampal longitudinal and transverse axes determined the number of their target areas and the spatial distribution and complexity of their axon arbors within the targets. We defined selective hippocampal subdomains based on spatial transcriptomic profiles and found that many projectome subtypes were enriched in specific subdomains. Next, we defined the wiring diagram for hippocampal neurons exclusively projecting to hippocampal formation (HPF) and those projecting to both intra- and extra-HPF targets with coordinated projection strengths. Furthermore, bi-hemispheric projecting hippocampal neurons generally projected to one pair of homologous targets with ipsilateral preference. These organization principles of single-neuron projectomes provide a structural basis for understanding diverse but coordinated functions of hippocampal neurons.

opencc-by-4.0Dec 2021View details →

FlyWire: Online community for whole-brain connectomics

A ground truth dataset for 3D neuron reconstruction from electron microscopy (EM) images of the fly whole-brain, created for our project FlyWire: A human-AI collaboration to map the fly connectome. For more information, please visit <a href="https://flywire.ai/">https://flywire.ai/</a>.   Citation FlyWire: Online community for whole-brain connectomics Dorkenwald et al. bioRxiv 2020.08.30.274225; doi: https://doi.org/10.1101/2020.08.30.274225   Dataset description <ul> <li>cremi_realigned.tar.gz <ul> <li>cremi_{a,b,c}_realigned.h5: re-aligned CREMI volumes (<a href="https://cremi.org/">https://cremi.org/</a>)</li> <li>cremi_b_realigned_new.h5: re-aligned CREMI B volume with de-novo annotation</li> </ul> </li> <li>focused.tar.gz <ul> <li>A set of densely annotated volumes covering diverse structures in the fly brain that are underrepresented in the CREMI volumes.</li> </ul> </li> <li>sparse.tar.gz <ul> <li>A set of sparsely annotated volumes covering tricky failure modes in the initial segmentation attempt.  Here intracellular structures are often oversegmented conservatively to prevent merge errors at the expense of introducing some split errors. </li> </ul> </li> <li>glia.tar.gz <ul> <li>Semi-automatically generated ground truth for glia detction. A set of subvolumes from the FlyWire segmentation was sampled from which human experts classified automatically generated segments into either neurons or glia, while existing merge errors were excluded from annotation.</li> </ul> </li> </ul>

opencc-by-4.0Dec 2014View details →

BRAIN Journal-Isolating the Norepinephrine Pathway Comparing Lithium in Bipolar Patients to SSRIs in Depressive Patients-Figure 2. Resting state neuroimaging findings illustrating the action of Lithium following whole brain

The axial, saggital, and coronal MRI activation maps illustrate increased delta frequency band neuronal activity in the 46 patients diagnosed with Bipolar Affective Disorder compared to 32 female patients diagnosed with Major Depressive Disorder of Depressive Episode. The Yellow/Orange shades indicate increased neuronal activity in the right Superior Frontal Gyrus (t=0.920, p=0.05060, BA 6, MNI X=20, Y=0, Z=70) and in the right Cingulate Gyrus (t=0.0846, BA 24, MNI X= 5, Y=0, Z=51). Structural anatomy is shown in grey scale (A – anterior; S – superior; P – posterior; L – left; R – right).

opencc-by-4.0Dec 2014View details →

BRAIN Journal-Isolating the Norepinephrine Pathway Comparing Lithium in Bipolar Patients to SSRIs in Depressive Patients-Figure 1. Resting state neuroimaging findings illustrating the action of Lithium following whole brain

The axial, saggital, and coronal MRI activation maps illustrate neuronal activity of 46 patients diagnosed with Bipolar Affective Disorder compared to 16 male patients diagnosed with Major Depressive Disorder of Depressive Episode. The Yellow/Orange shades indicate increased neuronal activity in the right Superior Temporal Gyrus (t=1.403, p=0.00780, BA 41, MNI X=45, Y= -35, Z=10) with activation also in the Fusiform Gyrus (t=1.26, BA 20, MNI X= 45, Y= -35, Z=10), the Parahippocampal Gyrus (t=1.29, BA 36, MNI X=45, Y= -35, Z=10). (b) Increased neuronal activity in the Cingulate Gyrus (t=1.06, BA 32, MNI X=45, Y= -35, Z=10). Structural anatomy is shown in grey scale (A – anterior; S – superior; P – posterior; L – left; R – right).

opencc-by-4.0Jun 2016View details →

BRAIN Journal-An Energy-Saving Concept of the Smart Building Power Grid with Separated Lines for Standby Devices-Figure 1. The whole-building switch concept for the power lines of standby devices

68 million houses in North America and Europe will be smart by 2019 (Kurkinen, 2016) with a compound annual growth rate of 37 % and 61 %, respectively. The smart equipment is usually installed together with an upgrade (e.g. aluminum wires are replaced by copper ones) of the power grid. In this case, additional power lines for standby devices are cabled, and the WBS concept is applied using one power switch only (see figure 1). For instance, the Songle high-power relay T90  can control the whole building electricity with load up to 30 A using NodeMcu Lua ESP8266 WiFi and/or Arduino Uno / Mega boards.

publicOct 2024View details →

Data from: Direct segmentation of cortical cytoarchitectonic domains using ultra-high-resolution whole-brain diffusion MRI

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publicFeb 2025View details →

Whole-brain mapping in adult zebrafish and identification of the functional brain network underlying the novel tank test

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publicApr 2024View details →

Data from: Whole-brain spatial organization of hippocampal single-neuron projectomes

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opencc-by-4.0Dec 2020View details →

Data sets comparing Ca(2+) dynamics in whole-cell and β-escin-based perforated patch clamp recordings in adult mouse brain slices.

# Hess-et-al-beta-escin-2020 Data of the "Data in Brief" article concerning the added buffer approach with beta-escin perforated patch. A joint work by: Simon Hess (`simon.hess@uni-koeln.de`), Christophe Pouzat (`christophe.pouzat@math.unistra.fr`), and Peter Kloppenburg (`peter.kloppenburg@uni-koeln.de`). ## Content This repository contains: - Directory `data_whole_cell` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the whole-cell configuration. - Directory `data_beta_escin` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the β-escin perforated patch clamp configuration.

opencc-by-4.0Nov 2024View details →

[Dataset for] Whole-brain meso-vein imaging in living humans using fast 7 T MRI

This dataset is associated with: <ul> <li>Gulban, Stirnberg, Tse, Pizzuti, Koiso, Archila-Melendez, Huber, Bollmann, Goebel, Kay, Ivanov, 2025. Whole-brain meso-vein imaging in living humans using fast 7 T MRI (Preprint).</li> </ul> This dataset is also used in: <ul> <li>Pizzuti, Bazin, Ivanov, Dresbach, Peter, Goebel, Gulban, 2024.  Multimodal laminar characterization of visual areas along the cortical hierarchy (Preprint).</li> </ul> More data are going to be be added as we progress with our manuscripts though their publications or upon request (please contact Omer Faruk Gulban).

dryad36/100

Data from: In vivo human whole-brain Connectom diffusion MRI dataset at 760 µm isotropic resolution (PART I)

This whole-brain in vivo diffusion MRI dataset was acquired at 760 µm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy subject. It was acquired using state-of-the-art acquisition hardware and advanced reconstruction to achieve high SNR at such resolution, including a high-gradient-strength Connectom scanner, a custom-built 64-channel phased-array coil, a personalized motion-robust head stabilizer, a recently developed SNR-efficient dMRI acquisition, and parallel imaging reconstruction with advanced ghost reduction algorithms. With its unprecedented high resolution, SNR and image quality, it could help explore the fine-scale structures of in vivo human brain, and further advance the understanding of human brain connectivity. This dataset can also be used as a test bed for further technical development of new modeling, sub-sampling strategies, denoising and processing algorithms for in vivo high resolution dMRI. Whole brain anatomical T1-weighted and T2-weighted images at submillimeter scale, field maps and the code for preprocessing pipeline are also made available in the repository.

opencc-zeroApr 2021View details →

opencc-by-4.0Mar 2022View details →

7T Whole Body DMI Proposal Preliminary Data (Brain, Liver, Muscle, Heart)

Deuterium 2H-MRSI preliminary spectra acquired in vivo (brain, liver, heart, muscle) using 3D chemical shift imaging. Matrix size: 16x16x14, 12 mm isotropic, TR=350 ms, TA= 14 min.

dryad36/100

Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period

Aim: Perioperative neurocognitive disorders (PND) occur frequently after surgery and anesthesia, especially in aged patients. Previous studies have shown multiple PND related mechanisms in the hippocampus, however, their relationships remain unclear. Meanwhile, the perioperative neuropathological processes are sophisticated and changeable, single period study could not reveal the accurate mechanisms. Thus, multiperiod whole-transcriptome study is necessary to elucidate the gene expression patterns during perioperative period. Methods: Aged C57BL/6 mice were subjected to exploratory laparotomy under sevoflurane anesthesia. Whole-transcriptome sequencing (RNA-seq analysis) was performed on the hippocampi from control condition (Con), 30 minutes (Day0), 2 days (Day2) and 7 days (Day7) after surgery. Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analyses, quantitative Real-Time PCR, immunofluorescence and fear conditioning test were also performed to elucidate the pathological processes and modulation networks during the period. Results: Through RNA-seq analysis, 328, 3597 and 4179 differentially expressed genes (DEGs) were screened out in intraoperative period (Day0 vs Con), early postoperative period (Day2 vs Day0) and late postoperative period (Day7 vs Day2). The involved GO biological processes were divided into 9 categories, and positive-regulated processes were more than negative-regulated ones. Seventy-four transcription factors were highlighted. The potential synaptic and neuroinflammatory pathways were constructed for Neurotransmitter, Synapse and Neuronal alteration categories with 9 DEGs (Htr1a, Rims1, Ezh2, etc.). The metabolic and mitochondrial pathways were constructed for Metabolism, Oxidative stress and Biological rhythm categories with 9 DEGs (Gpld1, Sirt1, Cry2, etc.). The blood-brain barrier and neurotoxicity related pathways were constructed for Blood-brain barrier, Neurotoxicity and Cognitive function categories with 10 DEGs (Mmp2, Itpr1, Nrf1, etc.). Conclusion: The results revealed gene expression patterns and modulation networks in the aged hippocampus during perioperative period, which provide insights into overall mechanisms and potential therapeutic targets for prevention and treatment of perioperative central nervous system diseases, such as PND, from the genetic level.

opencc-zeroJun 2022View details →