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28 results for “image stacks”
◂Fig. 3 Gynoecium of C. crenata %yellow frames), C. cf. grandicalyx %blue frames) and C. sinensis %pink frames; A, B stack shot images; C–K light microscopy; G polarised light; TS in horizontal orientation). A, B Anthetic female flower, calyx and corolla partly removed. B LS of gynoecium. C LS of functionally female flower %note strongly stained peripheral tissue of corolla, anther and gynoecium). D LS of gynoecium. E, F TS of functionally female flower %note strongly stained, peripheral tissue). G TS of functionally female flower %note crystal deposition). H LS of ovule %note stalked embryo sac). J TS of functionally male flower with non-functional ovules. K LS of functionally male flower %style lacking, original position indicated by an asterisk) %LS, longisection; TS, transverse section; a,anther; bs, basal septum; c, calyx; car, carpel; co, corolla; db, dorsal bundles; es, embryo sac; fs, false septum; lb, lateral bundles; o, ovule; stg, stigma; sty, style; t, trichomes; tt, transmission tissue; ut, peripheral, strongly stained tissue; vb, ventral bundles; vs, ventral slit) in Observations on flower and fruit anatomy in dioecious species of Cordia (Cordiaceae, Boraginales) with evolutionary interpretations
◂Fig. 3 Gynoecium of C. crenata %yellow frames), C. cf. grandicalyx %blue frames) and C. sinensis %pink frames; A, B stack shot images; C–K light microscopy; G polarised light; TS in horizontal orientation). A, B Anthetic female flower, calyx and corolla partly removed. B LS of gynoecium. C LS of functionally female flower %note strongly stained peripheral tissue of corolla, anther and gynoecium). D LS of gynoecium. E, F TS of functionally female flower %note strongly stained, peripheral tissue). G TS of functionally female flower %note crystal deposition). H LS of ovule %note stalked embryo sac). J TS of functionally male flower with non-functional ovules. K LS of functionally male flower %style lacking, original position indicated by an asterisk) %LS, longisection; TS, transverse section; a,anther; bs, basal septum; c, calyx; car, carpel; co, corolla; db, dorsal bundles; es, embryo sac; fs, false septum; lb, lateral bundles; o, ovule; stg, stigma; sty, style; t, trichomes; tt, transmission tissue; ut, peripheral, strongly stained tissue; vb, ventral bundles; vs, ventral slit)
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>
Example of Fluorescence Lifetime Imaging Microscopy (FLIM) image stack in .ptu format
<p>The dataset is a 3D stack of fluorescence lifetime imaging microscopy (FLIM) images in ptu format to be used as test and training data. It contains the original .lif file (1) with the stack and a single plane image (to be opened using LAS X and LAS X SMD FLIM), exported raw FLIM data in .ptu format of the stack (3) and the single plane (2a) (to be opened in software capable of reading .ptu files) as well as an intensity image in .tif format (2b) of the single plane for a quick sample overview.</p> <p>The sample is a cross-section of hazel (<em>Corylus avellana</em>) 'diclinous male flower t.s.' with Etzold staining provided by the company Zeiss (CZ 01/05). The dataset was generated using a Leica Stellaris 8 upright confocal laser scanning microscope using a 93x/1.4 glycerol immersion objective. Each image of the 65 slice stack with z step size of 0.287 µm contains 512 x 512 pixels with a pixel size of 0.078 µm x 0.078 µm. Excitation was done with a white-light laser at 491 nm and a laser pulse rate of 40 MHz and a pixel dwell time of 2.0875 µs. Images were acquired using a HyD X detector in counting mode in the spectral range of 496 to 739 nm using Leica Application Suite X (LAS X) version 4.4.0.24861 and LAS X SMD FLIM version 4.5.0 for FLIM image acquisition. 10 frames were accumulated per image. Metadata is available as text file (4a) and as metadata files from LAS X (4b).</p>
Image stacks for full-body transcription factor expression atlas with completely resolved cell identities in C. elegans
<p>Each image stack presented as zip file. Once decompressed, each folder contain '.ano' linker file, straightening C. elegans L1 images file, the segmentation mask image file and the cell annotation file. The image files are stored in Peng Hanchuan RAW/TIFF format, and the cell annotation file is stored in simple comma separated values format. To visualize the image stack data, drag the '.ano' linker file to VANO interface. </p> <p>vano_win32_1.741.zip contains VANO for worm visualization.</p>
Stacking microscopy images of the pteropod Limacina bulimoides
<p>Pteropods, a group of holoplanktonic gastropods, are regarded as bioindicators of the effects of ocean acidification on open ocean ecosystems, because their thin aragonitic shells are susceptible to dissolution. While there have been recent efforts to address their capacity for physiological acclimation, it is also important to gain predictive understanding of their ability to adapt to future ocean conditions. However, little is known about the levels of genetic variation and large scale population structuring of pteropods, key characteristics enabling local adaptation. We examined the spatial distribution of genetic diversity in the mitochondrial cytochrome <i>c</i> oxidase I (COI) and nuclear 28S gene fragments, as well as shell shape variation, across a latitudinal transect in the Atlantic Ocean (35°N-36°S) for the pteropod <i>Limacina bulimoides</i>. We observed high levels of genetic variability (COI π = 0.034, 28S π = 0.0021) and strong spatial structuring (COI Φ<sub>ST </sub>= 0.230, 28S Φ<sub>ST </sub>= 0.255) across this transect. Based on the congruence of mitochondrial and nuclear differentiation, as well as differences in shell shape, we identified a primary dispersal barrier in the southern Atlantic subtropical gyre (15-18°S). This barrier is maintained despite the presence of expatriates, a gyral current system, and in the absence of any distinct oceanographic gradients in this region, suggesting that reproductive isolation between these populations must be strong. A secondary dispersal barrier supported only by 28S pairwise Φ<sub>ST </sub>comparisons was identified in the equatorial upwelling region (between 15°N-4°S), which is concordant with barriers observed in other zooplankton species. Both oceanic dispersal barriers were congruent with regions of low abundance reported for a similar basin-scale transect that was sampled two years later. Our finding supports the hypothesis that low abundance indicates areas of suboptimal habitat that result in barriers to gene flow in widely-distributed zooplankton species. Such species may in fact consist of several populations or (sub)species that are adapted to local environmental conditions, limiting their potential for adaptive responses to ocean changes. Future analyses of genome-wide diversity in pteropods could provide further insight into the strength, formation and maintenance of oceanic dispersal barriers.</p>
Image stack, PLY-files and a NEX-file accompanying: A new symmoriiform from the Late Devonian of Morocco: novel jaw function in ancient sharks
<p>We describe the small chondrichthyan Ferromirum oukherbouchi n.gen. et sp. from the Famennian (Late Devonian) of the Maïder region in Morocco. This chondrichthyan is exceptionally well preserved and displays not only mineralized soft tissues but also undeformed cartilages of the head, gills, and shoulder girdle. A reconstruction of the head using 3D-prints revealed a previously unknown kind of jaw articulation. Here, we make the original cropped image stack and PLY-files of the single cartilaginous elements accessible. Additionally, a nexus-file with the character matrix used for the cladogram shown in the article is included.</p>
Entire confocal z-stack series as .tif image sequences
<p>The manuscript entitled "Parvalbumin-expressing ependymal cells in rostral lateral ventricle wall adhesions contribute to aging-related ventricle stenosis in mice" shows confocal z-stack maximum intensity projections and thin z-plane reconstructions in the figure plates. The entire confocal z-stack image series are provided here as .tif image sequences, respectively the confocal z-stacks of the negative controls as well. The file names refer to the figure numbers and position in the figure plates. For more information about the immunostaining and image acquisition, see the Materials & Methods and Figure legends in the manuscript.</p>
Speckle image stacks acquired on human skin with a high-speed camera
<p>These datasets all consist of stacks of images of various body parts of of the same 50-year-old Caucasian male subject.</p> <p>For each acquisition, the skin was first illuminated with a near-infrared LASER (wavelength 785 nm). Then, the skin was filmed with a Phantom VEO 710L camera, with an acquisition rate of 2000 to 30,000 Hz.</p> <ul> <li>Datasets <strong>WRIST_1</strong>, <strong>WRIST_2</strong> and <strong>WRIST_3</strong> were acquired by imaging the anterior surface of the left wrist, with respective acquisition frequencies of 3000, 2000 and 10,000 Hz.</li> <li>Dataset <strong>FINGERS</strong> consists of images of the end of two fingers of the left hand. It was acquired at 30,000 Hz.</li> <li>Dataset <strong>EAR</strong> consists of images of the right ear. It was acquired at 2000 Hz.</li> <li>Dataset <strong>PALM</strong> consists of images of the palm of the left hand, which was gently scraped beforehand to trigger a superficial inflammation and draw a smiley face. It was then filmed with an acquisition frequency of 10,000 Hz.</li> </ul> <p>Each dataset is stored in a HDF5 file. The data array is stored as <strong>data </strong>at the root of the tree structure. Attributes <strong>T_exp </strong>and <strong>f_acq</strong> provide respectively the exposure time (in microseconds) and the acquisition rate (in Hertz) of the dataset. The script <strong>test.py </strong>shows how data can be accessed through Python and the library h5py. It can be used as follows:</p> <pre><code class="language-bash">python test.py filename.h5</code></pre> <p>All these datasets are used and referenced in our companion article "Dynamic speckle imaging of human skin vasculature with a high-speed camera" (to be published).</p>
Tif Image Stack - Example of a long sequence that was split into two tif files
<p>These two tif files were recorded during a single time-series capture. </p> <p>20240723_uro3g_t000000.tif - This image stack contains 3984 frames (time slices)</p> <p>20240723_uro3g_t000001.tif - This image stack contains 324 frames (time slices).</p> <p>The total number of frames/time slices should be 4308. (3984 + 324)</p> <p> </p> <p> </p> <p> </p>
Example stacked images and best-fit dust SEDs.
<p>Example stacked images, shown in bins of stellar mass and redshift, for the Herschel SPIRE 500 μm band.</p> <p>Stacked far-IR photometry for the whole sample of galaxies (SEDs_all) and for the star-forming only (SEDs_SF). The best-fit<br>dust emission curves, adopted from Casey (2012), are shown in solid green with 1σ standard deviation in grey.</p>
Kirchhoff pre-stack depth migration images of the multi-channel seismic data, SO190, RV. SONNE
<p>The dataset consists of four newly processed 2-D pre-stack depth migrated multi-channel seismic lines (BGR06_303, BGR06_305, BGR06_311 and BGR06_313) collected by GEOMAR and BGR in 2006. The dataset reveals the subducted oceanic reliefs and detailed accretionary wedge structure offshore eastern Java, Bali, Lombok, and Sumbawa islands, along the Sunda arc. The dataset is saved in standard SEGY format and could be loaded in open-source or commercial software. </p>
Confocal image stacks of GFP expression in Drosophila forelegs driven by Gal4 driver expression in foreleg motor neurons
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Stacking microscopy images of the pteropod Limacina bulimoides
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Image stack, PLY-files and a NEX-file accompanying: A new symmoriiform from the Late Devonian of Morocco: novel jaw function in ancient sharks
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Confocal microscopy image stacks from "Temporal integration of auxin information for the regulation of patterning"
<p>This dataset contains raw images in CZI format (Zeiss) of shoot apical meristems (SAM) from <em>Arabidopsis thaliana </em>transgenic lines <strong>qDII-pCLV3-pDR5</strong> or <strong>qDII-pCLV3-PIN1</strong>. See <em>(Galvan-Ampudia and Cerutti et al.) </em>for detailed information. This data constitutes the input of the <strong>sam_spaghetti</strong> pipeline (<a href="https://gitlab.inria.fr/mosaic/publications/sam_spaghetti">https://gitlab.inria.fr/mosaic/publications/sam_spaghetti</a>) and can be processed using the scripts and examples provided in the package.</p> <p> </p> <p><strong>File information:</strong></p> <p>File names containing qDII-CLV3-DR5 have the following data:</p> <ul> <li>Channel 1: <em>DII-VENUS-N7</em></li> <li>Channel 2: <em>pDR5:2xmTurquoise2</em></li> <li>Channel 3: <em>pRPS5a:TagBFP-SV40</em></li> <li>Channel 4: <em>pCLV3:mCherry-N7</em></li> </ul> <p>File names containing qDII-CLV3-PIN1-PI have the following data:</p> <ul> <li>Channel 1: <em>DII-VENUS-N7</em></li> <li>Channel 2: <em>pPIN1:PIN1-GFP</em></li> <li>Channel 3: <em>Propidium Iodide (cell walls)</em></li> <li>Channel 4: <em>pRPS5a:TagBFP-SV40</em></li> <li>Channel 5: <em>pCLV3:mCherry-N7</em></li> </ul> <p>Time-lapse sequences are identified as follows:</p> <ul> <li><strong>qDII-CLV3-DR5-E27-LD-SAM7.czi</strong></li> <li><strong>qDII-CLV3-DR5-E27-LD-SAM7-T5.czi</strong></li> <li><strong>qDII-CLV3-DR5-E27-LD-SAM7-T10.czi</strong></li> </ul> <p>where:</p> <ul> <li><strong>qDII-CLV3-DR5</strong> indicates the line</li> <li><strong>E$$-LD</strong> (e.g. E25-LD, E27-LD, etc) indicates independent biological replicas</li> <li><strong>SAM$</strong> is the meristem (technical replica)</li> <li><strong>T$</strong> indicates the time elapsed after the first image (in hours)</li> </ul> <p>For example <strong>qDII-CLV3-DR5-E27-LD-SAM7-T5.czi</strong> is an image of the 7th SAM of the set E27, acquired 5 hours after the first image.</p>
Confocal image stack of aPKC/FoxP co-staining
<p>Confocal image stacks of whole mount preparations of central nervous systems of adult Drosophila.</p><p>Genotype: aPKC-Gal4>CD8::GFP, red - FoxP-LexA>CD8::RFP; D: green - D42-Gal4>CD8::GFP, red - FoxP-LexA>CD8::RFP. Confocal image stacks available at: </p>
Original CT image stacks of five fossil petrosal bones from Siberia, 3D PDF files of reconstructed endocasts, blood vessels and innervation patterns, 3D PDF instruction file, STL files of the petrosals
<p>Five partially preserved mammaliaform petrosals recovered from Middle Jurassic sediments of the Berezovsk coal mine (Krasnoyarsk Krai, Russia) show similarities to other early mammaliaforms like the morganucodontan <i>Morganucodon</i> and the docodontan <i>Haldanodon</i> in having an inflated promontorium, and a curved and apically inflated cochlear canal. But they are distinct from dryolestoid and derived mammalian petrosals by the weak coiling of the cochlear duct and the presence of a perilymphatic foramen with an open perilymphatic sulcus. The two larger and robust specimens exhibit striking similarities to docodontan petrosals. Inside the bone an intricate circumpromontorial venous plexus was discovered as recently described for the docodontan <i>Borealestes</i>, confirming this structure is consistently present in basal mammaliaforms. The three smaller and slender petrosals likely belong to haramiyidans and are unique in showing a septum-like structure medially along the cochlear nerve entrance. The protruding perforated bony bar that is preserved in two of the three is interpreted here to be a remnant of a bony septum with multiple foramina for cochlear nerve fibers, representing an autapomorphic feature of Haramiyida. This newly described passageway for nerve fibers shows that the formation of the osteological structure surrounding the nervous pathways of the cochlea is more plastic among the most basal mammaliaforms than previously thought.</p>
Removal of developmentally regulated microexons has a minimal impact on larval zebrafish brain morphology and function - imaging stacks
<p>Results of brain activity mapping for zebrafish mutants with microexons removed. Both brain activity and structural data is included. These stacks are the significant signal that differs between the groups. They are compatable with the Z-Brain matlab viewer from Randlett, et al, 2015 Nature Methods.</p>
Spectral and Z stack images of sofa eye zebrafish
<p>This is a z-stacks with spectral imaging acquired in a Confocal Zeiss 880 LSM Microscope at the Institut Psteur Montevideo.</p> <p>Samples correspond to the eye of sofa zebrafish.</p> <p>For more informatio about the Sofa line, please see the following reference.</p> <p>Almeida AD, Boije H, Chow RW, He J, Tham J, Suzuki SC, Harris WA. Spectrum of Fates: a new approach to the study of the developing zebrafish retina. Development. 2014 May;141(9):1971-80. doi: 10.1242/dev.104760. Epub 2014 Apr 9. Erratum in: Development. 2014 Jul;141(14):2912. PMID: 24718991; PMCID: PMC3994774.</p>
Data from: Comparing ant morphology measurements from microscope and online AntWeb.org 2D z-stacked images
<p><span>Unprecedented technological advances in digitization and the steadily expanding open-access digital repositories are yielding new opportunities to quickly and efficiently measure morphological traits without transportation and advanced/expensive microscope machinery. A prime example is the AntWeb.org database, which allows researchers from all over the world to study taxonomic, ecological, or evolutionary questions on the same ant specimens with ease. However, the reproducibility and reliability of morphometric data deduced from AntWeb compared to traditional microscope measurements has not yet been tested.</span></p> <p><span>Here, we compared 12 morphological traits of 46 <em>Temnothorax</em> ant specimens measured either directly by stereomicroscope on physical specimens or via the widely used open access software tpsDig utilizing AntWeb digital images. We employed a complex statistical framework to test several aspects of reproducibility and reliability between the methods. We estimated (i) the agreement between the measurement methods and (ii) the trait value dependence of the agreement, then (iii) compared the coefficients of variation produced by the different methods, and finally, (iv) tested for systematic bias between the methods in a mixed modelling-based statistical framework.</span></p> <p><span>The stereomicroscope measurements were extremely precise. Our comparisons showed that agreement between the two methods was exceptionally high, without trait value dependence. Further, the coefficients of variation did not differ between the methods. However, we found systematic bias in eight traits: apart from one trait where software measurements overestimated the microscopic measurements, the former underestimated the latter.</span></p> <p><span>Our results shed light on the fact that relying solely on the level of agreement between methods can be highly misleading. In our case, even though the software measurements predicted microscope measurements very well, replacing traditional microscope measurements with software measurements, and especially mixing data collected by the different methods, might result in erroneous conclusions. We provide guidance on the best way to utilize virtual specimens (2D z-stacked images) as a source of morphometric data, emphasizing the method's limitations in certain fields and applications.</span></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.