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39 results for “two-photon”
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>
Localization of protoporphyrin IX in glioma patients with paired stimulated Raman histology and two-photon 3 excitation fluorescence microscopy
<div> <div> <div> <h1>Spatially resolved transcriptomics</h1> <p>Tissue fixation was performed following the ‘Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols’ (CG000160 | Rev C), which included heating the slide and immersing it in pre-chilled methanol. In the tissue staining phase, isopropanol was applied to tissue sections followed by a series of air-drying, hema- toxylin application, washing, bluing buffer application, eosin mix addition, and further washing. The slide was then dried on a heating block. Imaging was conducted using the Evos microscope, with the settings following the previously described protocol. Permeabilization and reverse transcription were undertaken without a preceding tissue optimization on Visium Tissue Optimization Slides, as the optimal permeabiliza- tion time for brain tissue had been established at 12 minutes by a previous researcher. The overall library preparation adhered to the ‘Visium Spatial Gene Expression Reagent Kits – User Guide’ (CG000239 | Rev F). During permeabilization, the Visium slide with stained tissue sections was fitted into a slide cassette and exposed to permeabilization enzyme, followed by a wash with 0.1X SSC buffer. For reverse transcription, an RT master mix was dispensed into each well, followed by a 45-minute incubation period in a thermocycler at 53 ° Celsius. In the second strand synthesis stage, each well received an addition of 75 ul 0.08 M KOH, followed by a brief room-temperature incubation. Subsequently, wells were washed with buffer EB and re- ceived the second strand mix, before undergoing a 15-minute incubation at 65 ° Celsius in a thermocycler. The denaturation process involved washing the wells with buffer EB and adding 35 ul 0.08 M KOH in each well, which were then incubated at room temperature. Afterward, Tris 1 M pH 7.0 was pipetted into four tubes of an 8-tube strip, followed by a transfer of samples from each well into these tubes. The tubes were then vortexed, centrifuged, and placed on ice, with the remaining sample stored for subsequent stages. The experiment initiated with the determination of cycle number wherein a qPCR mix was allocated across five wells of a qPCR plate, with a negative control included. The ensuing qPCR and Cq determination followed the standard protocol used for FFPE methods. Notably, uneven Cq values starting from n.5 were rounded up. In the subsequent cDNA amplification phase, an amplification mix was introduced to each sample tube, followed by thermo-cycling for actual PCR using a specified protocol. The cDNA cleanup process involved adding a SPRIselect reagent to each sample tube, followed by a series of incubation, washing, drying, and buffer addition steps. The cleaned-up samples were then transferred to new tubes. Finally, cDNA quality control and quantification were performed using a Tape Station. The total cDNA yield was calculated, factoring in the library concentration and elution volume. The process of fragmentation, end repair, and A-tailing started with using just a quarter of the purified library, with the remaining portion stored at -20 ° Celsius. The selected volume was mixed with buffer EB and fragmentation mix and incubated in a thermal cycler. Double-sided size selection was performed to discard large fragments and retain fragments within the desired size range. This involved the use of SPRIselect reagent, and resulted in a library with reduced total volume and a smaller range of fragment sizes. Adaptor ligation involved mixing adaptor ligation mix with each sample and incubating in a thermocycler. Post-ligation cleanup followed the cleanup steps post-cDNA amplification, with minor adjustments to the quantities of SPRIselect reagent and buffer EB. Sample index PCR was then performed, with an amp mix and dual index TT set A added to each sample, followed by a specific PCR protocol. The total number of cycles was determined based on the cDNA yield. Another round of double-sided size selection was performed, this time with varied substance quantities, to ensure another cleanup stage. The process concluded with a post-library construction quality control, ensuring the success of the library construction. While no exact concentration calculations were necessary, the fragment size in base pairs was of interest. A Fragment Analyzer was used due to its availability and accuracy in fragment size calculation. Sequencing was performed on a NextSeq 550.</p> <h1>Postprocessing and analysis pipeline</h1> <p>The data analysis and quality control for this research was conducted using the 10X Genomics’ space ranger pipeline and the SPATA2 (version 2.0) framework for spatial data analysis. The SPATA2 object was initiated through the ‘SPATA2::initiateSpataObject_10X’ function. This import procedure involved several stages using the Seurat version 4.0 package. Firstly, gene expression normalization was performed by dividing each spot’s values by the estimated total number of transcripts. These normalized values were then multiplied by 10,000 and underwent a natural logarithm transformation to improve interpretability and comparability across genes. Next, a regression model was applied to remove batch effects and scale the data. This model factored in sample batch and the expression percentages of ribosomal and mitochondrial genes, helping to control for potential sources of unwanted variation in the data. For a more detailed understanding of this process, you can refer to the guide provided at this link: https://themilolab.github.io/SPATA2/. This guide provides comprehensive information about the SPATA2 package and its application in spatial transcriptomics analysis.</p> </div> </div> </div> <div> <div> <div> <h1>Postprocessing and imaging analysis</h1> <p>The H&E images along with the PpIX and SRH images were aligned using afine transformation as described recently. For classification of the PpIX patterns we extracted 160x160 sized patches from each barcode spot and predicted the pattern using the pretrained ResNet architecture.</p> </div> </div> </div>
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>
3D Real-Time Single Particle Tracking using two-photon fluorescence from bright dye-based organic nanoparticles
<p>Data set, and attached ReadMe files related to the production of the figures in the article "3D Real-Time Single Particle Tracking using two-photon fluorescence from bright dye-based organic nanoparticles" by Emperauger et al.</p> <p> </p> <p>The ReadMe files explaining how each data file is organised, the data are in txt format, organised by figure and sub-figures and compressed. </p>
Two-photon calcium recordings of cones
<p>For colour vision, retinal circuits separate information about intensity and wavelength. This requires circuit-level comparison of at least two spectrally distinct photoreceptors. However, many vertebrates use all four 'ancestral' photoreceptors ('red', 'green', 'blue', 'UV'), and in those cases the nature and implementation of this computation remains poorly understood. Here, we establish the complete circuit architecture of outer retinal circuits underlying colour processing in the tetrachromatic larval zebrafish, which involves all four ancestral cone types and three types of horizontal cells. Our findings reveal that the synaptic outputs of red- and green-cones efficiently rotate the encoding of natural daylight in a principal component analysis (PCA)-like manner to yield primary achromatic and spectrally-opponent axes, respectively. Together, these two cones capture 91.3% of the spectral variance in natural light. Next, blue-cones are tuned so as to capture most remaining variance when opposed to green-cones. Finally, UV-cones present a UV-achromatic axis for prey capture. We note that fruit flies – the only other tetrachromat species where comparable circuit-level information is available - use essentially the same strategy to extract spectral information from their relatively blue-shifted terrestrial visual world. Together, our results suggest that rotating colour space into primary achromatic and chromatic axes at the eye's first synapse may be a fundamental principle of colour vision when using more than two spectrally well-separated photoreceptor types.</p>
Nondegenerate two-photon absorption in ZnSe: Experiment and theory
<p>Dataset of the publication “Nondegenerate two-photon absorption in ZnSe: Experiment and theory“, L. Krauss-Kodytek, W.-R. Hannes, T. Meier, C. Ruppert, and M. Betz, <a href="https://doi.org/10.1103/PhysRevB.104.085201">Phys. Rev. B 104, 085201 (2021).</a> ( <a href="https://doi.org/10.1103/PhysRevB.104.085201">https://doi.org/10.1103/PhysRevB.104.085201</a> ). The zip file includes the data on which the plots shown in figures 3, 4, and 5 are based.</p>
Two-photon absorption and second harmonic generation of 1S para- and orthoexcitons in Cu2O coupled by a magnetic field
<p>Dataset of the publication “Two-photon absorption and second harmonic generation of 1S para- and orthoexcitons in Cu2O coupled by a magnetic field“, (https://doi.org/10.1103/PhysRevB.102.115203). The xlsx file includes the measured datapoints on which the plots shown in figures 3, 4, 6-9 of the main text are based.</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)
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Label-free imaging of M1 and M2 macrophage phenotypes in the human dermis in vivo using two-photon excited FLIM
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Two-photon calcium recordings of cones
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Ultrafast two-photon fluorescence imaging of cerebral blood circulation in the mouse brain in vivo
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In-vivo two-photon imaging of aberrant Ca2+-waves following viral transduction of Ca2+ indicators in mice
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5D-NP-FABTECH_FNH - Open Dataset for "Facile Handling of 3D Two-Photon Polymerized Microstructures by Ultra-Conformable Freestanding Polymeric Membranes"
<p>This is the open dataset for the paper: "Frank Marco den Hoed, Ottomaniello Andrea, Omar Tricinci, Luca Cesarecciu, Marco Carlotti, Patrizio Raffa and Virgilio Mattoli, Facile Handling of 3D Two-Photon Polymerized Microstructures by Ultra-Conformable Freestanding Polymeric Membranes, On line (2023) [DOI:10.5281/zenodo.7837976]".</p> <p>This include the Supplementary Information file ("Supplementary-Info-AdvFuncMater_denHoed-Ottomaniello_2023.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>
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
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tRNA analysis and two-photon imaging of a 5,000-year-old human femur
GEO Series GSE85722. Homo sapiens. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Local recovery of cardiac calcium-induced calcium release interrogated by ultra- effective, two-photon uncaging of calcium
<p>The ZIP files contain all the confocal line-scan images (.oif files) organized by date. The analysis is illustrated in the respective PDF files. The Excel file contains a single entry with description and calculated parameters for each of the 12'157 analyzed events. </p>
Reversing the Warburg Effect by Promoting Oxidative Phosphorylation Reduces Glioblastoma Growth as Assessed by Two-Photon Microscopy
<p><strong>Supplementary Materials:</strong>The following are available online at www.mdpi.com/xxx/s1, Video S1: The GB cell line U87GFP+ co-cultured with organotypic brain slices demonstrated without treatment tumor growth and invasion as quantified by two-photon fluorescence microscopy, 3Dview-A.mp4; Video S2: Following treatment, i.e. reversing the Warburg effect, the tumor keeps the original size and spheric shape without any signs of invasion, 3Dview-B.mp4.</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.