Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
21
datasets available to search
ShareScore release 0.7.1
Dataset results
21 results for “two-photon imaging”
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>
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>
Data from: Microprism-based two-photon imaging of the mouse inferior colliculus reveals novel organizational principles of the auditory midbrain
Open the record for dataset details and reuse information.
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>
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
Open the record for dataset details and reuse information.
Simultaneous two-photon voltage or calcium imaging and multi-channel LFP recordings in barrel cortex of awake and anesthetized mice
Open the record for dataset details and reuse information.
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>
Fast wavefront shaping for two-photon brain imaging with multi-patch correction - raw datas
<p>Raw stack images for the main figures of the paper: "Fast wavefront shaping for two-photon brain imaging with multi-patch correction" </p>
Analysis code for two-photon imaging data
<p>They are the analysis code in the manuscript 'Modulation of cortical representations of sensory and contextual information underlies aversive associative learning'.</p>
Label-free imaging of M1 and M2 macrophage phenotypes in the human dermis in vivo using two-photon excited FLIM
<p>Macrophages (ΜΦs) are important immune effector cells that promote (M1 ΜΦs) or inhibit (M2 ΜΦs) inflammation and are involved in numerous physiological and pathogenic immune responses. Their precise role and relevance, however, are not fully understood for lack of non-invasive quantification methods. Here, we show that two-photon excited fluorescence lifetime imaging (TPE-FLIM), a label-free non-invasive method, can visualize ΜΦs in the human dermis in vivo. We demonstrate in vitro that human dermal ΜΦs exhibit specific TPE-FLIM properties that distinguish them from the main components of the extracellular matrix and other dermal cells. We visualized ΜΦs, their phenotypes and phagocytosis in the skin of healthy individuals in vivo using TPE-FLIM. Additionally, machine learning identified M1 and M2 MФs with a sensitivity of 0.88±0.04 and 0.82±0.03 and a specificity of 0.89±0.03 and 0.90±0.03, respectively. In clinical research, TPE-FLIM can advance the understanding of the role of MФs in health and disease.</p>
Serial two-photon tomography (STPT) of the brain through bi-channel image registration and deep learning segmentation (BIRDS)
Open the record for dataset details and reuse information.
Label-free imaging of M1 and M2 macrophage phenotypes in the human dermis in vivo using two-photon excited FLIM
Open the record for dataset details and reuse information.
Ultrafast two-photon fluorescence imaging of cerebral blood circulation in the mouse brain in vivo
Open the record for dataset details and reuse information.
In-vivo two-photon imaging of aberrant Ca2+-waves following viral transduction of Ca2+ indicators in mice
Open the record for dataset details and reuse information.
Data from: High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging in vivo
Optical imaging has become a powerful tool for studying brains in vivo. The opacity of adult brains makes microendoscopy, with an optical probe such as a gradient index (GRIN) lens embedded into brain tissue to provide optical relay, the method of choice for imaging neurons and neural activity in deeply buried brain structures. Incorporating a Bessel focus scanning module into two-photon fluorescence microendoscopy, we extended the excitation focus axially and improved its lateral resolution. Scanning the Bessel focus in 2D, we imaged volumes of neurons at high-throughput while resolving fine structures such as synaptic terminals. We applied this approach to the volumetric anatomical imaging of dendritic spines and axonal boutons in the mouse hippocampus, and functional imaging of GABAergic neurons in the mouse lateral hypothalamus in vivo.
Data from: High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging in vivo
Open the record for dataset details and reuse information.
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.