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39
datasets available to search
ShareScore release 0.9.0
Dataset results
39 results for “two-photon”
Data set for "Axonal and dendritic morphology of excitatory neurons in layer 2/3 mouse barrel cortex imaged through whole-brain two-photon tomography and registered to a digital brain atlas"
<p>Data set for: Liu Y, Foustoukos G, Crochet S and Petersen CCH (2022) Axonal and dendritic morphology of excitatory neurons in layer 2/3 mouse barrel cortex imaged through whole-brain two-photon tomography and registered to a digital brain atlas. Front Neuroanat 15: 791015. https://doi.org/10.3389/fnana.2021.791015</p> <p>There are 2 files in this upload:</p> <p>1. The file named "<strong>2022_Liu_FrontNeuroanat.pdf</strong>" is the Open Access pdf of the online publication in Frontiers in Neuroanatomy.</p> <p>2. The file named "<strong>Liu_data_code.zip</strong>" (~1 GB) is a zipped version of a folder ‘<em>Liu_data_code</em>’, which contains the data analyzed in the study along with the Python codes used to generate the published figures. The original high resolution image stacks obtained through whole-brain two-photon serial tomography are unfortunately too large for Zenodo, and only highly-downsampled data are included in this upload, which were used for registration with the Allen CCFv3. Instructions on how to view and analyse the anatomical data are provided in the 'README.docx' file, which you will find upon unzipping the folder.</p> <p> </p>
Data supporting 3D Super-resolution Optical Fluctuation Imaging with Temporal Focusing with two-photon excitation
<p>Data to support the publication combining temporal focusing two photon excitation with super-resolution optical fluctuation imaging.</p> <div>This research was funded by National Centre of Science, grant number: 2022/47/B/ST7/03465. For the purpose of Open Access, the author has applied a</div> <div>CC-BY public copyright licence to any author Accepted Manuscript (AAM) version arising from this submission</div>
Dataset of Axon Segmentation and Centerlines, Acquired using a Two-photon Microscope in the Live Mouse Cortex
<p>This dataset contains 20 images of real axons that were published previously in Bass et al (2017). This subset dataset has been added labels of binary images for segmentation of the axons, and of centerline for tracing of the axons.</p> <p>We provide the following:</p> <ul> <li>Images-MAX: 2D images of axons (.png)</li> <li>Images-TIFF: 3D images of axons (.tiff)</li> <li>Labels-binary: Manual segmentation of the axons as binary images (.png)</li> <li>Labels-tracing: Manual tracing of the axons (.swc)</li> </ul> <p>This data was collected in the live mouse cortex, using a two-photon microscope, with a 40x objective, at zoom 4, and with a resolution of 512 × 512 pixels, 0.147 <em>μ</em>m per pixel for the <em>x</em>, <em>y</em> planes, and 1 <em>μ</em>m for the <em>z</em> plane. . </p> <p><strong>Please cite the following papers when using this dataset:</strong></p> <p>T. Dai, M. Dubois, K. Arulkumaran, J. Campbell, B. Billot, C. Bass, Z. Uslu, V. De Paola, C. Clopath, and A. A. Bharath. Deep reinforcement learning for subpixel neural tracking. <em>Medical Imaging with Deep Learning</em>. 2019.</p> <p>Bass C, Helkkula P, De Paola V, Clopath C, Bharath AA. Detection of axonal synapses in 3D two-photon images. Giniger E, ed. <em>PLoS ONE</em>. 2017;12(9):e0183309. doi:10.1371/journal.pone.0183309.</p>
Two-photon fluorescence microscopy image stacks of human brain sections (grey and white matter)
<p>Two-photon fluorescence microscopy (TPFM) image stacks of human brain sections including grey matter (N<sub>g</sub>=10) and white matter (N<sub>w</sub>=10), considered in the validation of the 3D fiber orientation analysis pipeline proposed in: "<em>Fiber enhancement and 3D orientation analysis in label-free two-photon fluorescence microscopy</em>". <br> Human brain tissue was preliminarily treated for TPFM following the label-free MAGIC preparation technique, presented in (Costantini et al., <em>Scientific Reports</em> 2021).</p> <p>The PSF of the TPFM system has a FWHM of (0.692, 0.692, 2.612) μm along the x, y, and z axes, respectively, whereas the adopted voxel size is 0.88 μm x 0.88 μm x 1 μm.</p>
5D-NP-FABTECH_FSG - Open Dataset for "Highly Conformable Terahertz Metasurface Absorbers via Two-photon Polymerization on Polymeric Ultra-thin Films"
<p>This is the open dataset for the paper: "Ottomaniello Andrea, Paolo Vezio, Omar Tricinci, Frank Marco den Hoed, Paul Dean, Alessandro Tredicucci and Virgilio Mattoli, Highly Conformable Terahertz Metasurface Absorbers via Two-photon Polymerization on Polymeric Ultra-thin Films, On line (2023) [DOI:10.5281/zenodo.7838033]".</p> <p>This include the Supplementary Information file ("suppl_j_nanoph-2022-0667_suppl.pdf"), all the source material used for the paper preparation and more. </p> <p>For each folder (sub-dataset) there is a corresponding readme file describing the content and including metadata</p>
Time/frequency-domain characterization of a mid-IR DFG frequency comb via two-photon and heterodyne detection: datasets
<p>This archive contains the datasets used for generating the plots shown in the paper entitled "Time/frequency-domain characterization of a mid-IR DFG frequency comb via two-photon and heterodyne detection", authored by Tecla Gabbrielli, Giacomo Insero, Michele De Regis, Nicola Corrias, Iacopo Galli, Davide Mazzotti, Paolo Bartolini, Jeong Hyun Huh, Carsten Cleff, Alexander Kastner, Ronald Holzwarth, Simone Borri, Luigi Consolino, Paolo De Natale, and Francesco Cappelli. </p> <p>A README file describing the contained data and how to elaborate them is also provided. </p> <p> </p>
Dataset: Frequency-Dependent Quadratic Response Properties and Two-photon Absorption from Relativistic Equation-of-Motion Coupled Cluster Theory
<p>This dataset comprises outputs and post-processing results related to the paper "Frequency-Dependent Quadratic Response Properties and Two-photon Absorption from Relativistic Equation-of-Motion Coupled Cluster Theory", by Xiang Yuan, Loic Halbert, Lucas Visscher and Andre Severo Pereira Gomes.</p>
Data from: Open-top Bessel beam two-photon light sheet microscopy for three-dimensional pathology
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Data from: Microprism-based two-photon imaging of the mouse inferior colliculus reveals novel organizational principles of the auditory midbrain
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Dataset of Axonal Synapses, Acquired using a Two-photon Microscope in the Live Mouse Cortex
<p>This Dataset consists of TIFF 100 images, split in 20 test and 80 training images, of axons with their synapses (boutons) labelled. The labels are in form of ground-truth binary images of the same size, in which the corresponding synapses have been labelled as boxes.</p> <p>This data was collected in the live mouse cortex, using a two-photon microscope, with a 40x objective, at zoom 4, with a resolution of 512 x 512 x 0.147 microns per pixel, and a Point Spread Function characterised by a Full Width at Half Maximum (FWHM) values of 0.45 x 0.45 x 2.5 microns (x, y, z). </p> <p> </p> <p><strong>Please cite the following paper when using this dataset:</strong></p> <p>Bass C, Helkkula P, De Paola V, Clopath C, Bharath AA. Detection of axonal synapses in 3D two-photon images. Giniger E, ed. <em>PLoS ONE</em>. 2017;12(9):e0183309. doi:10.1371/journal.pone.0183309.</p> <p> </p>
Raw data for "Deep mouse brain two-photon near-infrared fluorescence imaging using a superconducting nanowire single-photon detector array"
<p>Two-photon microscopy (2PM) has become an important tool in biology to study the structure and function of intact tissues in-vivo. However, adult mammalian tissues such as the mouse brain are highly scattering, thereby putting fundamental limits on the achievable imaging depth, which typically resides around 600-800um. In principle, shifting both the excitation as well as (fluorescence) emission light to the shortwave near-infrared (SWIR, 1000-1700 nm) region promises substantially deeper imaging in 2PM, yet has proven challenging in the past due to the limited availability of detectors and probes in this wavelength region. To overcome these limitations and fully capitalize on the SWIR region, in this work we introduce a novel array of superconducting nanowire single-photon detectors (SNSPDs) and associated custom detection electronics for the use in near-infrared 2PM. The SNSPD array exhibits high efficiency and dynamic range, as well as low dark-count rates over a wide wavelength range. Additionally, the electronics and software permit seamless integration into typical 2PM systems. Together with a fluorescent dye emitting at 1105 nm, we report imaging depth of > 1.1mm in the in-vivo mouse brain, limited only by available labeling density and laser power. Our work further establishes SWIR 2PM approaches and SNSPDs as promising technologies for deep tissue biological imaging. </p>
Simultaneous two-photon voltage or calcium imaging and multi-channel LFP recordings in barrel cortex of awake and anesthetized mice
<p>Neuronal population activity, both spontaneous and sensory-evoked, generates propagating waves in cortex. However, high spatiotemporal-resolution mapping of these waves is difficult as calcium imaging, the work horse of current imaging, does not reveal subthreshold activity.</p> <p>Here, we present a platform combining voltage or calcium two-photon imaging with multi-channel local field potential (LFP) recordings in different layers of the barrel cortex from anesthetized and awake head-restrained mice. A chronic cranial window with access port allows injecting a viral vector expressing GCaMP6f or the voltage-sensitive dye (VSD) ANNINE-6plus, as well as entering the brain with a multi-channel neural probe. We present both average spontaneous activity and average evoked signals in response to multi-whisker air-puff stimulations.</p> <p>Time domain analysis shows the dependence of the evoked responses on the cortical layer and on the state of the animal, here separated into anesthetized, awake but resting, and running. The simultaneous data acquisition allows to compare the average membrane depolarization measured with ANNINE-6plus with the amplitude and shape of the LFP recordings. The calcium imaging data connects these data sets to the large existing database of this important second messenger. Interestingly, in the calcium imaging data, we found a few cells which showed a decrease in calcium concentration in response to vibrissa stimulation in awake mice.</p> <p>This system offers a multimodal technique to study the spatiotemporal dynamics of neuronal signals through a 3D architecture in vivo. It will provide novel insights on sensory coding, closing the gap between electrical and optical recordings.</p>
Source data for "Non-Telecentric two-photon microscopy for 3D random access mesoscale 2 imaging"
<p>Source data used in a manuscript "Non-Telecentric two-photon microscopy for 3D random access mesoscale 2 imaging"</p> <p> </p> <p> </p> <p> </p>
IN SILICO SCREENING OF TWO-PHOTON ABSORPTION PROPERTIES OF A LARGE SET OF BIS-BF2-DYES
<p>This data set is a part of Supporting Info for our work entitled “IN SILICO SCREENING OF TWO-PHOTON ABSORPTION PROPERTIES OF A LARGE SET OF BIS-BF2-DYES” which is published in ChemPhotoChem peer-reviewed scientific journal (<a href="https://doi.org/10.1002/cptc.202200137">doi.org/10.1002/cptc.202200137</a>). In this data set, we provide the XYZ coordinates for the 280 compounds studied in this work.</p>
Scanless two-photon voltage imaging example code and dataset
<p>This data and code are associated with the manuscript "Scanless two-photon voltage imaging" published in Nature Communications in June 2024 (DOI: <a href="10.1038/s41467-024-49192-2">10.1038/s41467-024-49192-2</a><span>). </span></p>
Two-photon imaging of D1 and D2 type neurons in the olfactory tubercle of behaving mice
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Simultaneous two-photon voltage or calcium imaging and multi-channel LFP recordings in barrel cortex of awake and anesthetized mice
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Data for: Multiplexed miniaturized two-photon microscopy (M-MINI2Ps)
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Raw data accompanying the manuscript "Super-resolution fluorescence microscopy by line-scanning with an unmodified two-photon microscope"
<p>Raw data sets (.tif files) of data utilized to demonstrate 2D SIM with an unmodified multi photon intravital fluorescence microscope.</p>
Serial two-photon tomography (STPT) of the brain through bi-channel image registration and deep learning segmentation (BIRDS)
<p>We have developed an open-source software called BIRDS (bi-channel image registration and deep learning segmentation) for the mapping and analysis of 3D microscopy data and applied this to the mouse brain. The BIRDS pipeline includes image pre-processing, bi-channel registration, automatic annotation, creation of a 3D digital frame, high-resolution visualization, and expandable quantitative analysis. This new bi-channel registration algorithm is adaptive to various types of whole-brain data from different microscopy platforms and shows dramatically improved registration accuracy. Additionally, as this platform combines registration with neural networks, its improved function relative to other platforms lies in the fact that the registration procedure can readily provide training data for network construction, while the trained neural network can efficiently segment incomplete/defective brain data that is otherwise difficult to register. Our software is thus optimized to enable either minute-timescale registration-based segmentation of cross-modality, whole-brain datasets or real-time inference-based image segmentation of various brain regions of interest. Jobs can be easily submitted and implemented via a Fiji plugin that can be adapted to most computing environments.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.