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.
74
datasets available to search
ShareScore release 0.9.0
Dataset results
74 results for “brain morphology”
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>
Fluorescent Microglia Images for Analyzing Morphological Changes due to Injury Duration in the Ischemic Rat Brain
<p>The image data included in this dataset are the confocal microscope images (converted from original .nd2 file to .tiff form) used for the publication: Joseph, A., Liao, R., Zhang, M., Helmbrecht, H., McKenna, M., Filteau, J. R., & Nance, E. (2020). Nanoparticle-microglial interaction in the ischemic brain is modulated by injury duration and treatment. <em>Bioengineering & translational medicine</em>, <em>5</em>(3), e10175. https://doi.org/10.1002/btm2.10175</p> <p>The data is organized by brain slice number, region, and image number. There is also an included excel file 'datadescriptions.xlsx' that provides more information about the metadata of the dataset. </p> <p> </p> <p>The data was procured and processed by the Disease Directed Engineering Lab, PI: Elizabeth Nance, at the University of Washington.</p>
Shifting balances in the weighting of sensory modalities are predicted by divergence in brain morphology in incipient species of Heliconius butterflies
<p>Integrating and weighting sensory perception across modalities is crucial to how animals adapt to their environment. Divergence in brain structure is often in sensory processing regions, suggesting that investment reflects ecological needs. Here, we use two parapatric closely related species, <em>Heliconius erato cyrbia</em> and <em>Heliconius himera</em>, to test the hypothesis that divergence in sensory brain regions affects foraging decisions. These butterflies are isolated across an ecological gradient, which is linked to differences in brain morphology, with <em>H. e. cyrbia </em>investing more in visual centres and <em>H. himera</em> investing in olfactory centres. Here, we demonstrate that these two species vary in how they associate visual and olfactory cues with positive food rewards. We found that when individuals were trained on paired olfactory and visual stimuli, then presented with these stimuli in conflict, they showed distinct behavioural responses. <em>Heliconius himera</em> was more likely to favour positive olfactory cues than <em>H. e. cyrbia</em>, which favoured visual cues regardless of the paired stimulus. This suggests that these species have diverged in the emphasis placed on these different sensory domains during foraging, consistent with observed differences in brain morphology. This result strengthens evidence that speciation initiated by local adaptation is partly facilitated by changes in the neural basis of key behavioural functions.</p>
Figure 11. Nervous system and brain. A in Systematics, evolution and phylogeny of Annelida - a morphological perspective
Figure 11. Nervous system and brain. A. Nervous system of the trunk with longitudinal and segmental circular nerves exemplified by Parapodrilus psammophilus (Dorvilleidae). Ventral cord consists of unpaired median (mn) and main paired nerves (mvn). B-D. Anti α-tubulin immunoreactivity; dotted lines indicate segment borders. B. Polygordius appendiculatus (Polygordiidae), ventral nerve cord (green) comprising three closely apposed neurite bundles, serotonergic perikarya (red) in a repetitive pattern although distinct ganglia are absent (medullary cord). Note high number of segmental nerves. C-D. Brania clavata (Syllidae); depth coding images. C. Brain (b) and ventral nerve cord in ventral view, ventral cord consists of several closely apposed nerves forming 3 bundles behind 1st ganglion (g1), 4 segmental nerves (arrowheads, ppn) in each segment; brain gives rise to several stomatogastric nerves (sn). D. Ventral cord in the trunk region. F. General diagram of the cephalic nervous system in polychaetes, numerals refer to palp nerve roots, somata stippled. E-H. Nereis sp. (Nereididae). E Ventral nerve cord in basiepithelial position (arrowheads refer to epidermal extracellular matrix). F. Parasagittal section with mushroom bodies (mb), note subepithelial position of brain; arrowheads point to cerebral ganglia. H Enlargement of anterior part of mushroom body with stalks of globuli cells (gc). – br = brain, cc = circumoesophageal connective, dcdr = dorsal commissure of drcc, dcvr = dorsal commissure of vrcc, dlln = dorsolateral longitudinal nerve, drcc = dorsal root of cc, ecm = extracellular matrix, ep = epidermis, g1 = 1st ganglion, gc = globuli cell, in = intestine, lln = lateral longitudinal nerve, mb = mushroom body, mn = median nerve of ventral cord, mvn = main nerve of ventral cord, nla = nerve of lateral antenna, nma = nerve of median antenna, no = nuchal organ, np = neuropil, obm = oblique muscle, pn = palp nerve, ppn = parapodial nerve, sn = stomatogastric nerve, so = somata of neurites, sog = suboesophageal ganglion, vbv = ventral blood vessel, vcdr = ventral commissure of drcc, vcvr = ventral commissure of vrcc, vlm = ventral longitudinal muscle, vrcc = ventral root of cc. A, F: modified from Müller and Orrhage (2005). Micrographs; B C: Lehmacher, C, D: M. Kuper, Osnabrück.
Fig. 6 in The brain of Brycon orbignyanus (Valenciennes, 1850) (Teleostei: Characiformes: Bryconidae): gross morphology and phylogenetic considerations
Fig. 6. Olfactory epithelium of representatives of Otophysi. a. Cyprinus carpio (Cypriniformes); b. Brycon orbignyanus (Characiformes); c. Pimelodus maculatus (Siluriformes) and; Sternopygus macrurus (Gymnotiformes). Scale bars = 1 mm.
Fig. 5 in The brain of Brycon orbignyanus (Valenciennes, 1850) (Teleostei: Characiformes: Bryconidae): gross morphology and phylogenetic considerations
Fig. 5. Brain of Gymnotus carapo (Gymnotiformes: Gymnotidae), LIRP 7767, 129.0 mm SL. a. dorsal; b. lateral and c. ventral views. Apt = Area postrema; Bol = bulbus olfactorius; Ch = chiasma opticum; Cocb = corpus cerebelli; Dien = diencephalon; Eg = eminentia granularis; ELL = electrosensory lateral line lobus; Hl = lateral nucleus of hypotalhamus; Hyp = hypophysis; LobX = lobus vagi; Mo = medulla oblongata; Ms = medulla spinalis; ndl = lateral portion of nucleus diffusus; nE = nucleus electrosensorius; Sv = saccus vasculosus; Tect = tectum opticum; Tv = tela ventriculi; Vcocb = valvula cerebellum. Cranial Nerves: nI = nervus olfactorius; nII = nervus opticus; nV = nervus trigeminus; nVI = nervus abducens; nVII = nervus fascialis; nVIII = nervus octavus; nlla = nervus lineae lateralis anterior; nllp = nervus lineae lateralis posterior; nIX = nervus glossopharyngeus; nX = nervus vagus.
Fig. 2 in The brain of Brycon orbignyanus (Valenciennes, 1850) (Teleostei: Characiformes: Bryconidae): gross morphology and phylogenetic considerations
Fig. 2. Brain of Brycon orbignyanus (Characiformes: Bryconidae), LIRP 6309, 175.5 mm SL. a. dorsal; b. lateral and c. ventral views. Apt = Area postrema; Bol = bulbus olfactorius; Ch = chiasma opticum; Cocb = corpus cerebelli; Dien = diencephalon; Eg = eminentia granularis; Hyp = hypophysis; Hyt = hypothalamus; Lih = lobus inferior hypothalami; LobX = lobus vagi; Mo = medulla oblongata; Ms = medulla spinalis; Pob = nervus tractus olfactorius; Sv = saccus vasculosus; Tect = tectum opticum;; Telen = Telencephalon Tl = Torus lateralis; Tv = tela ventriculi; Cranial Nerves: nI = nervus olfactorius; nII = nervus opticus; nIII = nervus oculomotorius; nIV = nervus trochlearis; nV = nervus trigeminus; nVI = nervus abducens; nVII = nervus fascialis; nVIII = nervus octavus; nLLa = nervus lineae lateralis anterior; nLLp = nervus lineae lateralis posterior; nIX = nervus glossopharyngeus; nX = nervus vagus and; nSo = nervus spino-occipitales.
Fig. 1 in The brain of Brycon orbignyanus (Valenciennes, 1850) (Teleostei: Characiformes: Bryconidae): gross morphology and phylogenetic considerations
Fig. 1. Brain of Brycon orbignyanus (Characiformes: Bryconidae), LIRP 6309, 175.5 mm SL. Main encephalic divisons (Telencephalon, Diencephalon, Mesencephalon, Rhombencephalon + Medulla oblongata and Medulla spinalis) in different colors. a. dorsal; b. lateral and c. ventral views.
Fig. 3 in The brain of Brycon orbignyanus (Valenciennes, 1850) (Teleostei: Characiformes: Bryconidae): gross morphology and phylogenetic considerations
Fig. 3. Brain of Cyprinus carpio (Cypriniformes: Cyprinidae), LIRP 8923, 72.3 mm SL. a. dorsal; b. lateral and c. ventral views. Apt = Area postrema; Bol = bulbus olfactorius; Ch = chiasma opticum; Cocb = corpus cerebelli; Dien = diencephalon; Eg = eminentia granularis; Hyp = hypophysis; Hyt = hypothalamus; Lih = lobus inferior hypothalami; LobVII = lobus facialis; LobX = lobus vagi; Mo = medulla oblongata; Ms = medulla spinalis; Pob = nervus tractus olfactorius; Tect = tectum opticum; Telen = Telencephalon; Tl = Torus lateralis; Tv = tela ventriculi. Cranial Nerves: nI = nervus olfactorius; nII = nervus opticus; nIII = nervus oculomotorius; nIV = nervus trochlearis; nV = nervus trigeminus; nVI = nervus abducens; nVII = nervus fascialis; nVIII = nervus octavus; nlla = nervus lineae lateralis anterior; nllp = nervus lineae lateralis posterior; nIX = nervus glossopharyngeus; nX = nervus vagus and; nSo = nervus spino-occipitales.
Fig. 4 in The brain of Brycon orbignyanus (Valenciennes, 1850) (Teleostei: Characiformes: Bryconidae): gross morphology and phylogenetic considerations
Fig. 4. Brain of Diplomystes mesembrinus (Siluriformes: Diplomystidae), LBP 449, 72.62 mm SL. a. dorsal; b. lateral and c. ventral views. Apt = Area postrema; Bol = bulbus olfactorius; Ch = chiasma opticum; Cocb = corpus cerebelli; Dien = diencephalon; Eg = eminentia granularis; Hyp = hypophysis; Hyt = hypothalamus; Lih = lobus inferior hypothalami; LobVII = lobus facialis; LobX = lobus vagi; Mo = medulla oblongata; Ms = medulla spinalis; Pob = nervus tractus olfactorius; Tect = tectum opticum; Telen = Telencephalon; Tl = Torus lateralis; Tv = tela ventriculi. Cranial Nerves: nI = nervus olfactorius; nII = nervus opticus; nIII = nervus oculomotorius; nIV = nervus trochlearis; nV = nervus trigeminus; nVI = nervus abducens; nVII = nervus fascialis; nVIII = nervus octavus; nlla = nervus lineae lateralis anterior; nllp = nervus lineae lateralis posterior; nIX = nervus glossopharyngeus; nX = nervus vagus and; nSo = nervus spino-occipitales.
Alteration of cleaner wrasse cognition and brain morphology under marine heatwaves
Open the record for dataset details and reuse information.
Data from: Shifting balances in the weighting of sensory modalities are predicted by divergence in brain morphology in incipient species of Heliconius butterflies
Open the record for dataset details and reuse information.
Natural and anthropogenic sources of habitat variation influence exploration behaviour, stress response, and brain morphology in a coastal fish
<p>1. Evolutionary ecology aims to better understand how ecologically important traits respond to environmental heterogeneity. Environments vary both naturally and as a result of human activities, and investigations that simultaneously consider how natural and human-induced environmental variation affect diverse trait types grow increasingly important as human activities drive species endangerment.</p> <p>2. Here, we examine how habitat fragmentation and structural habitat complexity, affect disparate trait types in Bahamas mosquitofish (<em>Gambusia hubbsi</em>) inhabiting tidal creeks. We tested a priori predictions for how these factors might influence exploratory behaviour, stress reactivity, and brain anatomy.</p> <p>3. We examined approximately 350 adult Bahamas mosquitofish from seven tidal creek populations across Andros Island, The Bahamas that varied in both human-caused fragmentation (three fragmented, four unfragmented) and natural habitat complexity (e.g. 5-fold variation in rock habitat).</p> <p>4. Populations that had experienced severe human-induced fragmentation, and thus restriction of tidal exchange from the ocean, exhibited greater exploration of a novel environment, stronger physiological stress responses to a mildly stressful event, and smaller telencephala (relative to body size). These changes matched adaptive predictions based mostly on 1) reduced chronic predation risk and 2) decreased demands for navigating tidally dynamic habitats. Populations from sites with greater structural habitat complexity showed a higher propensity for exploration and a relatively larger optic tectum and cerebellum. These patterns matched adaptive predictions related to increased demands for navigating complex environments.</p> <p>5. Our findings demonstrate environmental variation, including recent anthropogenic impacts (<50 years), can significantly affect complex, ecologically important traits. Yet trait-specific patterns may not be easily predicted, as we found strong support for only six of 12 predictions. Our results further highlight the utility of simultaneously quantifying multiple environmental factors—e.g. had we failed to account for habitat complexity, we would not have detected effects of fragmentation on exploratory behaviours. These responses, and their ecological consequences, may be complex: rapid and adaptive phenotypic responses to anthropogenic impacts can facilitate persistence in human-altered environments, but may come at a cost of population vulnerability if ecological restoration were to occur without consideration of the altered traits. </p>
Data from: Convergent avialan brain morphology in Sinovenator (Troodontidae, Theropoda)
<p><em>Sinovenator changii</em> IVPP V20378 is a troodontid theropod dinosaur from the Early Cretaceous strata in Liaoning, northeastern China. The specimen is a nearly complete 3D-preserved skeleton. The postcranial elements are in sleeping posture and the skull is isolated from the rest. The skull suffered only slight deformation and distortion, completely preserving most of its elements except the left postorbital, parietal, and squamosal. The dataset comprises three .stl files of the skull, brain endocast, and inner ear of <em>Sinovenator changii</em> IVPP V20378. </p>
The evolution of plasticity in brain morphology following colonization of an ecologically divergent habitat in Trinidadian guppies
<p>Natural environments are constantly changing. To survive, organisms will either need to rapidly adapt to new conditions or colonize new habitats. Colonization has been hypothesized to select for increased plasticity as well as increased brain size, though empirical tests of these effects have proven difficult to evaluate. In particular, the degree to which plasticity of brain morphology can evolve, and its subsequent ecological consequences have rarely been explored. Trinidadian guppies (<em>Poecilia reticulata</em>) are known for their repeated adaptation to ancestral high-predation (HP) and derived low-predation (LP) environments. We used this system to examine the evolution and plasticity of brain morphology. We exposed second-generation offspring of individuals collected from HP and LP sites to two different kinds of environmental treatments: predation cues and conspecific social environment. We found that guppies descended from a colonized LP habitat showed greater plasticity in brain morphology than descendants of their ancestral HP population, supporting the hypothesis that plasticity of brain morphology may increase fitness after colonization of a novel habitat. Additionally, we show sexual dimorphism in brain morphology plasticity. Overall, these results suggest the evolution of brain morphology plasticity as an important mechanism that allows for ecological diversification and colonization of novel habitats.</p>
Derived brain morphology measures from CamCAN data
<p>Derived brain morphology measures from CamCAN data.</p>
Figure 2 in Gross brain morphology of Rhamdia quelen (Quoy & Gaimard 1824) (Ostariophysi: Siluriformes: Heptapteridae)
Figure 2. Brain of Rhamdia quelen, MZUEL 6036, 222.37 mm SL, in (a) dorsal, (b) lateral and (c) ventral views. Scale bar = 1 mm.
Figure 4 in Gross brain morphology of Rhamdia quelen (Quoy & Gaimard 1824) (Ostariophysi: Siluriformes: Heptapteridae)
Figure 4. Details brain regions of species of Heptapteridae in dorsal view. (a) Pimelodella gracilis, MZUEL 1574; (b) Imparfinis mirini, MZUEL 4028; (c) Rhamdia quelen, MZUEL 6036; (d) Imparfinis mirini, MZUEL 4028. White arrows indicate the position of tectum mesencephali in relation to telencephalon. Red arrows indicate the position of lateral line lobe in relation to lobus vagi. Scale bar = 1 mm.
Figure 1 in Gross brain morphology of Rhamdia quelen (Quoy & Gaimard 1824) (Ostariophysi: Siluriformes: Heptapteridae)
Figure 1. Camera lucida drawing of the brain and neurocranium of an adult specimen of Rhamdia quelen, MZUEL 7418, 64.03 mm SL, in dorsal (a) and ventral (b) views. a.f: anterior fontanel; ap: autopalatine; boc: basioccipital; bol: bulbus olfactorius; ep: epiotic; exc: extracapula; exo: exoccipital; fr: frontal; l.et: lateral ethmoid; ma: maxilla; me: mesethmoid; nII: nervus opticus; nV: nervus trigeminus; nVII: nervus facialis; nVIII: nervus octavus; nX: nervus vagus; na: nasal; nllp: nervus lineae lateralis posterior; of: olfactory organ; os: orbitosphenoid; pa: parasphenoid; p.f: posterior fontanel; p.m: premaxillary; pro: prootic; ps: pterosphenoid; pt: pterotic; soc: supraoccipital; socp: supraoccipital process; sph: sphenotic; tol: tractus olfactorius; vo: vomer. Scale bar = 1 mm.
Figure 3 in Gross brain morphology of Rhamdia quelen (Quoy & Gaimard 1824) (Ostariophysi: Siluriformes: Heptapteridae)
Figure 3. Brain of species of Heptapteridae in dorsal view. (a) Cetopsorhamdia iheringi, MZUEL 2260; (b) Goeldiella eques, MZUEL 7417; (c) Heptapterus mustelinus, MZUEL 5074; (d) Imparfinis mirini, MZUEL 4028; (e) Pimelodella gracilis, MZUEL 1574; (f) Phenacorhamdia tenebrosa, MZUEL 2706; (g) Rhamdia quelen, MZUEL 6036. Scale bar = 1 mm.
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.