Biology subjects

Kaneko, T.

Publications and source records attributed to Kaneko, T..

17 recordsLinked to original sources

bioRxiv2026

Genotype-dependent reductions of competition are associated with yield maintenance in a modern common wheat Triticum aestivum L. cultivar

Modern crop breeding has increased yield under monoculture stands, but the mechanisms underlying this improvement remain incompletely understood. We tested whether genotype-dependent reduction of competition, whereby plants adjust competitive responses according to neighbor genetic identity, contributes to yield maintenance in modern common wheat cultivars. We conducted a root-exudate application experiment and two competition experiments using three common wheat (Triticum aestivum L.) landraces and one modern cultivar, Norin 61. Norin 61 exhibited little change in shoot-to-root allocation in response to root exudates from the same cultivar compared with distilled water, whereas it increased shoot-to-root allocation exposed to root exudate from different cultivars. Moreover, shoot-to-root allocation increased with decreasing genetic relatedness between neighboring cultivars in common wheat plants. In competition experiments, greater shoot-to-root allocation was associated with stronger suppression of competitors. Norin 61 maintained grain biomass under the same-cultivar competition compared to solitary conditions but exhibited substantial yield reductions when competing with different cultivars, whereas these patterns were weaker or absent in landraces. These results suggest that genotype-dependent reduction of competition may contribute to yield maintenance in modern wheat cultivars and provide a new perspective on how crop breeding has shaped plant-plant interactions in monoculture stands.

ecology↗

bioRxiv2026

Social behaviours predict vocal turn-taking in common marmosets

Human conversation depends on the continuous integration of vocal exchanges with visual and spatial cues, yet the evolutionary origins of this multimodal coordination remain poorly understood. Although vocal turn-taking has been documented across many animal species, studies have largely examined vocal exchanges in isolation from the accompanying social dynamics. Using acoustic localization and 3D pose tracking in freely interacting marmoset pairs, we simultaneously quantified vocal behaviour and social interactions during natural communication. We found that vocal turn-taking is dependent on distinct multimodal behavioural states defined by head orientation, spatial proximity, and ongoing social interaction. While call features did not reliably predict turn-taking, these behavioural dynamics predicted whether vocal exchanges developed into turn-taking or terminated after isolated calls. Our findings reveal that primate vocal communication is fundamentally organized by multimodal behavioural coordination rather than by vocal signals alone, providing an evolutionary framework for understanding the origins of human conversation.

neuroscience↗

bioRxiv2026

A Novel Metric for Quantifying the Sustainability of Phage-Mediated Bacterial Suppression

The global spread of antimicrobial-resistant (AMR) bacteria represents one of the greatest threats to modern medicine, making the development of novel therapeutic strategies increasingly urgent. Phage therapy, which exploits bacteriophages (phages, viruses that specifically infect and kill bacteria) has regained attention as a therapeutic approach for multidrug-resistant infections. One critical determinant of treatment outcome is the capacity of phages to sustain bacterial growth suppression; however, no metric has previously existed to directly quantify the duration of effective lytic activity. Here, we propose the Sustainability Index (SusI), a novel metric that quantifies both the duration and extent of phage-mediated bacterial growth suppression, which is restricted to the primary lysis period from lysis initiation to resistance emergence. Evaluation of individual phages and two-phage cocktails against both laboratory and clinical isolates of Escherichia coli demonstrated that SusI provides information independent of the Virulence Index, which primarily reflects bactericidal activity during the initial phase of infection, and serves as a complementary metric to the Suppression Index, which may incorporate behavior beyond primary lysis. Cocktails composed of phages targeting different receptors specificities consistently exhibited higher SusI values, consistent with the notion that multifaceted selective pressure delays resistance emergence. Furthermore, in a mouse model of systemic infection established by intraperitoneal administration, cocktails with higher SusI values demonstrated superior therapeutic efficacy. These results confirm SusI as a practical metric for rational phage cocktail design. As phage therapy advances toward clinical implementation, standardized quantitative metrics such as SusI are expected to facilitate evidence-based selection of therapeutic phages across diverse pathogens and infection conditions. ImportanceThe global spread of antimicrobial-resistant bacteria is making bacterial infections increasingly difficult to treat. Phage therapy, which uses bacteriophages (viruses that specifically infect bacteria), has re-emerged as a therapeutic alternative; however, reliable methods to determine in advance which phages will be therapeutically effective remain limited. Current evaluation metrics are well-suited for quantifying how rapidly phages kill bacteria but were not designed to directly measure how long lytic activity is sustained before resistant bacteria emerge. Here, we developed the Sustainability Index (SusI), a novel metric that specifically quantifies the duration of effective bacterial growth suppression. Evaluation of multiple phages and their combinations (cocktails) against both laboratory and clinical bacterial isolates demonstrated that SusI can distinguish phage combinations that existing metrics fail to differentiate. Moreover, in a mouse model of lethal bacterial infection, higher SusI values correlated with improved therapeutic outcomes. SusI has potential as a practical tool for selecting phages with greater likelihood of therapeutic success.

microbiology↗

bioRxiv2026

A multimodal dataset for reconstructing common marmoset body-environment interactions in a 3D digital-twin framework

The common marmoset (Callithrix jacchus) is an important non-human primate model in neuroscience and biomedical research. However, existing 3D resources for this species have mainly focused on brain atlases or keypoint-based pose estimation, and reusable data resources that jointly describe the body surface, fur, articulated structure, and experimental environment remain limited. Here, we present a multimodal dataset designed to reconstruct body- environment interactions of common marmosets in three dimensions. The dataset includes a whole-body surface mesh derived from computed tomography (CT) images, fur representations based on photographic references, a rigged 3D model for pose-driven animation, synchronized behavioral videos from three individuals recorded for approximately 90 hours from eight view-points, 2D and 3D keypoint estimation data, 3D models of the experimental environment constructed from blueprint information, and rendered pseudo-egocentric views generated by integrating pose estimation results with the 3D body and environment models. Technical validation assessed the geometric agreement between the CT-derived mesh and the surface model, the accuracy of 2D and 3D keypoint estimation, the dimensional accuracy of the environment model, and the structural similarity between real and rendered images. This dataset provides a foundation for treating marmoset natural behavior not only as point trajectories but also as a three-dimensional phenomenon involving body shape and its spatial relationship with the environment, thereby enabling applications in behavioral analysis, visualization, synthetic-data generation, and future digital-twin studies.

animal behavior and cognition↗

bioRxiv2026

Monju: Multi-criteria clustering in single-cell omics

Clustering is a fundamental step in single-cell omics analysis. Although single-cell omics data can, in principle, be partitioned according to multiple biologically meaningful criteria, existing methods typically cluster cells using a single criterion. To address this problem, we developed Monju, a multi-criteria clustering method based on a deep generative mixture model. Monju divides cells into biologically reasonable submodels, each of which is equipped with an interpretable latent space. Furthermore, although the partitioning of cells into submodels varies across random seeds, each solution remains biologically plausible, collectively yielding multi-criteria clustering. Moreover, by integrating these multiple clustering solutions to perform meta-clustering, Monju enables the assessment of cluster stability. We applied Monju to human peripheral blood CITE-seq data and demonstrated that it can achieve multi-criteria clustering. Monju therefore provides a powerful and practical framework for dissecting cellular heterogeneity from multiple biological perspectives.

bioinformatics↗

bioRxiv2026

Stress Granules and FUS condensates recruit functionally distinct sets of RNAs

Cellular homeostasis relies on the organization of RNA and protein into membrane-less organelles. Stress granules (SGs) are well-known hubs for translational repression during cellular stress. Similar condensates formed by RNA-binding proteins such as FUS-- mutations in which cause amyotrophic lateral sclerosis (ALS)--remain poorly characterized relative to canonical SGs. Here, we develop Granule-seq, a microcapillary-based granule-resolved RNA sequencing approach, and demonstrate that SGs and FUS condensates are functionally distinct RNA compartments rather than variants of a unified granule class. Granules were individually aspirated, analyzed in small pooled sets, and validated through overlap with known SG components (794/2,759 genes, 28.8%, p < 0.001). Gene Ontology analysis revealed that G3BP-positive SGs sequester transcripts for stress responses and translational control, while FUS condensates are enriched for transcripts essential for synaptic function and neuronal development. Direct comparison showed that 63% of FUS-enriched and 82% of G3BP-enriched genes were granule-specific, with only 493 genes shared. Exploratory sequence analysis revealed modest contributions from compositional features, with functional identity providing primary selectivity. As a proof-of-concept study with limited biological replication, our results suggest that distinct granule identities are established through functionally specialized transcriptomes, a process that may be disrupted in ALS, and provide a framework for understanding RNA sorting. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/726389v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1378da9org.highwire.dtl.DTLVardef@35906borg.highwire.dtl.DTLVardef@9c7880org.highwire.dtl.DTLVardef@ab3b9d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic abstract.C_FLOATNO Granule-seq workflow and key findings.(Left) Individual cytoplasmic granules are isolated by microcapillary aspiration, pooled ([~]10 granules per replicate), and processed for RNA sequencing alongside total-cell input. (Middle) Venn diagram showing the overlap between FUS condensate-enriched (1,334 genes) and G3BP1 stress granule-enriched (2,759 genes) transcripts. FUS condensates preferentially recruit neuronal and synaptic transcripts; G3BP1 stress granules are enriched for stress-response and proteostasis transcripts. (Right) Two-step recruitment model: shared sequence features (long 3'UTR, GC-rich composition, stable RNA structure) provide permissiveness for granule entry (Step 1), while RBP interactome composition and functional context determine granule-type specificity (Step 2). C_FIG

molecular biology↗

bioRxiv2026

Deep Microbial Colonization in 2-Billion-Year-Old Ultramafic Rock from the Bushveld Complex

Archean cratons may provide stable microbial habitats in the deep subsurface, as evidenced by the discovery of billion-year-old crustal fluids1,2. However, the long-term habitability of these cratonic environments is uncertain, as polymetamorphic evolution in most cratons typically destroys microbial habitats through mineral reactions and porosity loss3,4. Preservation of deep microbial habitats is more likely where mantle-derived magma intruded the craton after metamorphic overprinting4. Here we report the discovery of dense microbial colonization at 814 m depth within the 2.05-billion-year-old, unmetamorphosed Bushveld Igneous Complex intrusion, South Africa5. Using advanced contamination-control protocols6,7 and synchrotron-based X-ray spectroscopy, we identified indigenous microbial cells localized at the rims of phlogopite, a hydrous phyllosilicate mineral. Our study reveals that microbial colonization is associated with Fe(III) derived from the structure of phlogopite, where the dehydrogenation likely oxidizes Fe(II) to Fe(III) coupled to H2 generation8. Despite the absence of fracture-driven fluid ingress in the unfractured rock matrix, aqueous alteration evidenced at the rims by potassium removal indicates a self-sustaining habitat driven by an internal redox gradient9. These findings demonstrate that aqueous alteration of ultramafic rocks can sustain isolated microbial life over geological timescales, significantly expanding the potential for long-term habitability on both Earth and Mars4,10.

microbiology↗

bioRxiv2026

Chlamylipo, a Chlamydomonas-in-liposome microswimmer: self-propelled swimming and associated lipid membrane flow

Developing active transport systems for microcargo delivery is challenging and requires overcoming the low Reynolds number constraints. We developed a bio-hybrid micro-swimmer, "chlamylipo" consisting of the green alga Chlamydomonas reinhardtii, encapsulated within a giant liposome. Although internal encapsulation offers cargo protection, it requires a mechanism to transmit the propulsion force across a closed membrane. We demonstrated that chlamylipo exhibited forward swimming and phototactic directional control. High-speed imaging of membrane shape and fluid flow revealed that the driving force originated from periodic membrane deformations and was accompanied by characteristic fluid dynamics. Flow analysis showed rapid oscillations at tens of hertz corresponding to flagellar beating, superimposed on slower axial migration at approximately 4 Hz associated with cell rotation. Corresponding flow signatures were also detected in the external fluid, indicating mechanical coupling across the lipid bilayer. Membrane domain tracking further showed that fluid motions inside and outside the membrane were coupled through viscous friction and membrane deformation, generating a characteristic four-vortex flow field consistent with a two-point force model. Together, these results suggest that membrane flow mainly reflects force transmission across the bilayer, whereas forward propulsion is primarily driven by periodic membrane deformation. This study elucidates the physical mechanism of force transmission in encapsulated swimmers, demonstrating that internal hydrodynamic power can effectively drive the motion of macroscopic containers. SignificanceThe development of autonomous micro-swimmers for targeted drug delivery is a major challenge in biophysics. We present "chlamylipo," a hybrid system in which a swimming alga is encapsulated inside a lipid vesicle. This study is significant because it demonstrates that an enclosed swimmer can propel a macroscopic container solely via hydrodynamic coupling across a closed membrane without direct external mechanical links. Furthermore, we achieved external directional control using phototaxis. This study provides physical insights into fluid-membrane interactions and proposes a novel strategy for designing light-guided active transport carriers.

biophysics↗

bioRxiv2025

LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance

Chronic myeloid leukemia (CML) resistance to BCR-ABL tyrosine kinase inhibitors (TKIs) can arise from ABL kinase domain mutations, BCR-ABL fusion gene amplification, or kinase-independent mechanisms. To investigate imatinib-resistance, we performed quantitative mass spectrometry comparing the proteome and phosphoproteome of K562 cells (a standard CML model) and ImR cells, an imatinib-resistant K562 derivative that also exhibits cross-resistance to second- and third-generation BCR-ABL TKIs. In addition to revealing global proteome and phosphoproteome changes associated with drug resistance, we identified LIN28A--a multi-functional RNA-binding protein--as a critical mediator of imatinib resistance. LIN28A was significantly overexpressed and hyperphosphorylated in ImR cells. Depleting LIN28A via shRNA restored imatinib sensitivity, while its ectopic expression in parental K562 cells induced imatinib resistance. Mechanistically, LIN28A coordinates an extensive kinase-substrate network regulating proliferation, survival, and metabolism to drive resistance. Notably, pharmacological inhibition of LIN28A-dependent kinases (PKC, AKT, SGK1, and RPS6K) suppressed ImR proliferation. Midostaurin, a clinical PKC/FLT3 inhibitor used in FLT3-ITD--positive AML, potently re-sensitized ImR cells to imatinib. Our findings suggest that targeting LIN28A and its downstream effectors, particularly PKC, could overcome resistance to imatinib and next-generation BCR-ABL inhibitors.

cancer biology↗

bioRxiv2025

Novel Escherichia coli Phages Representing a Distinct Genus within Stephanstirmvirinae: Genome and Host Range Characteristics

Bacteriophages play crucial roles in microbial ecosystems and have potential biotechnological applications. However, our understanding of culturable phages remains limited. This study characterized six novel Escherichia coli phages isolated from pig farm wastewater and urban sewage using comprehensive genomic, morphological, and host-range analyses. Using multiple comparative approaches, including gene-sharing network analysis, average nucleotide identity (ANI), and nucleotide intergenomic similarity (NIS), we demonstrated that five of these phages form a distinct group within the subfamily Stephanstirmvirinae, potentially representing a novel genus provisionally named "Wecvirus". These phages were further classified into two distinct species within the proposed genus, each of which exhibits a unique host range pattern. This host specificity is reflected in the species-specific differences in the amino acid sequences of tail fibers, which are crucial for infection. The remaining phage, which was not classified as Wecvirus exhibited characteristics that challenged the current classification criteria, highlighting the need for more flexible taxonomic approaches. Our findings expand the understanding of phage diversity within Stephanstirmvirinae and contribute to the evolving phage taxonomy framework. ImportanceThe rapid emergence of antibiotic-resistant pathogens necessitates the development of alternative antimicrobial strategies, with phage therapy showing promising potential. However, the successful implementation of phage-based treatments requires a comprehensive understanding of phage diversity and host-pathogen interactions. Our study expands the known diversity within Stephanstirmvirinae by characterizing novel E. coli phages that constitute a distinct genus. The identification of species-specific host recognition mechanisms within this genus provides insights into phage-host adaptation. These findings contribute to our understanding of phage taxonomy and evolution, while also offering practical implications for the development of phage-based therapeutics against pathogenic E. coli strains. This research highlights the importance of continued exploration of novel phages for both fundamental understanding and therapeutic applications.

evolutionary biology↗

bioRxiv2024

From phenotype to receptor: validating physiological clustering of Escherichia coli phages through comprehensive receptor analysis

Understanding the relationship between bacteriophage (phage) classification and target receptors is crucial for phage ecology and applied research. In this study, we compared 13 previously isolated Escherichia coli phages based on physiological characteristics, whole-genome sequences, and tail fiber protein phylogenetics. We improved our previously proposed physiological clustering method by optimizing the bacterial panel for host range assessment, implementing appropriate distance metrics for mixed data types, and applying silhouette coefficient analysis for objective determination of optimal cluster numbers. We combined genomic analysis and lipopolysaccharide (LPS) structural analysis of phage-resistant E. coli strains to identify target receptors of the phages. Complementation experiments further confirmed the direct involvement of identified genes in phage reception. The results revealed that phylogenetically distinct E. coli phages target different sites in the LPS R-core region (modified by WaaV, WaaW, WaaT, and WaaY), membrane proteins (NfrB, TolA, YhaH), or flagella. Our analysis revealed that, subtle chemical modifications of LPS (such as Heptose phosphorylation) were shown to be important for E. coli phage recognition. Furthermore, physiological characteristics, tail fiber phylogenetics, and whole genome analysis independently classified the phages with high correlation to target receptor specificity. The addition of three phages with known receptors further validated our approach. Our results suggest that grouping based on physiological characteristics (such as lysis dynamics and host range) and genotypes (tail fiber phylogenetics or whole genome analysis) independently classified phages with high correlation to target receptor specificity. Here, we elucidated the diversity and specificity of E. coli phage target receptors, providing new insights into the classification of E. coli phages and phage-host interactions. ImportancePhage therapy is gaining attention as an alternative treatment for antibiotic-resistant bacteria. Developing effective phage cocktails requires combining phages with different target receptors, but traditional methods for identifying target receptors are labor-intensive. This study demonstrates that E. coli phages targeting the TK001 strain with different target receptors can be grouped based on their physiological characteristics, tail fiber sequences, or whole genomes. Our approach was enhanced through systematic bacterial panel selection for host range assessment, optimized distance metrics for physiological characteristics, and objective cluster determination using silhouette coefficient analysis for all three classifications. This insight can be used to more efficiently create diverse phage cocktails. Additionally, we identified phages targeting diverse sites, including different regions of LPS, membrane proteins, and flagella. These findings deepen our understanding of phage host recognition mechanisms, enabling the rapid preparation of effective phage cocktails and contributing to new advancements in bacterial infection treatment.

microbiology↗

bioRxiv2024

Investigating EMT-mediated resistance to EGFR tyrosine kinase inhibitors in NSCLC using innovative organoid models

BackgroundEpithelial-mesenchymal transition (EMT) has emerged as a key mechanism underlying resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) in EGFR-mutant non-small cell lung cancer (NSCLC). However, the intricacies of EMT-mediated resistance, driven by tumor microenvironment (TME) interactions, remain enigmatic. This study aimed to probe EMT-induced resistance in NSCLC using innovative in vitro organoid models. MethodsWe generated organoids by co-culturing EGFR-mutant NSCLC cells (HCC827, H1975), mesenchymal stem cells and endothelial cells. Drug susceptibility was compared between organoids and spheroids (cancer cells only) using EGFR TKIs - Gefitinib, Afatinib, Osimertinib. EMT marker (E-cadherin, ZEB1) expression was analyzed via immunofluorescence and western blotting. The effects of Bevacizumab and miR200c on overcoming resistance were also investigated. ResultsThe study identified a significant link between EMT and EGFR-TKI resistance. Notable findings included the decrease of E-cadherin and an increase in ZEB1, both of which influenced EMT and resistance to treatment. Bevacizumab showed promise in improving drug resistance and mitigating EMT, suggesting an involvement of the VEGF cascade. Transfection with miR200c was associated with improved EMT and drug resistance, further highlighting the role of EMT in TKI resistance. ConclusionsThis study offered vital insights into EMT-driven EGFR TKI resistance, highlighting the utility of organoid models in evaluating resistance modulated by TME interactions. Our findings reveal promising directions for overcoming EMT-mediated resistance involving Bevacizumab and miR200c, warranting further in vivo validation.

cancer biology↗

bioRxiv2023

Establishing an AI-based evaluation system that quantifies social/pathophysiological behaviors of common marmosets

Nonhuman primates (NHPs) are indispensable animal models by virtue of the continuity of behavioral repertoires across primates, including humans. However, behavioral assessment at the laboratory level has so far been limited. By applying multiple deep neural networks trained with large-scale datasets, we established an evaluation system that could reconstruct and estimate three-dimensional (3D) poses of common marmosets, a small NHP that is suitable for analyzing complex natural behaviors in laboratory setups. We further developed downstream analytic methodologies to quantify a variety of behavioral parameters beyond simple motion kinematics, such as social interactions and the internal state behind actions, obtained solely from 3D pose data. Moreover, a fully unsupervised approach enabled us to detect progressively-appearing symptomatic behaviors over a year in a Parkinsons disease model. The high-throughput and versatile nature of our analytic pipeline will open a new avenue for neuroscience research dealing with big-data analyses of social/pathophysiological behaviors in NHPs.

neuroscience↗

bioRxiv2023

Position-independent refinement of vagus motor neuron wiring

Motor neurons in the central nervous system often lie in a continuous topographic map, where neurons that innervate different body parts are spatially intermingled. This is the case for the efferent neurons of the vagus nerve, which innervate diverse muscle and organ targets in the head and viscera for brain-body communication. It remains elusive how neighboring motor neurons with different fixed peripheral axon targets develop the separate somatodendritic (input) connectivity they need to generate spatially precise body control. Here we show that vagus motor neurons in the zebrafish indeed generate spatially appropriate peripheral responses to focal sensory stimulation even when they are transplanted into ectopic positions within the topographic map, indicating that circuit refinement occurs after the establishment of coarse topography. Refinement depends on motor neuron synaptic transmission, suggesting that an experience-dependent periphery-to-brain feedback mechanism establishes specific input connectivity amongst intermingled motor populations.

neuroscience↗

bioRxiv2023

Three-dimensional markerless motion capture of multiple freely behaving monkeys for automated characterization of social behavior

Given their high sociality and close evolutionary distance to humans, monkeys are an essential animal model for unraveling the biological mechanisms underlying human social behavior and elucidating the pathogenesis of diseases exhibiting abnormal social behavior. However, behavioral analysis of naturally behaving monkeys requires manual counting of various behaviors, which has been a bottleneck due to problems in throughput and objectivity. Here, we developed a three-dimensional markerless motion capture system that utilized multi-view data for robust tracking of individual monkeys and accurate reconstruction of the three-dimensional poses of multiple monkeys living in groups. Validation analysis in two monkey groups revealed that the system enabled the characterization of individual social dispositions and relationships through automated detection of various social events. Analyses of social looking facilitated the investigation of adaptive behaviors in a social group. These results suggest that this motion capture system will significantly enhance our ability to analyze primate social behavior.

animal behavior and cognition↗

bioRxiv2022

Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range

Magnetic resonance imaging (MRI) is a noninvasive neuroimaging method beneficial for the identification of normal developmental and aging processes and data sharing. Marmosets have a relatively shorter life expectancy (approximately 10 years) than other primates, including, humans because they grow and age faster. Hence, the common marmoset model is effective in aging research. The current study investigated the aging process of the marmoset brain and provided an open MRI database on marmosets with a wide age range. The Brain/MINDS Marmoset Brain MRI Dataset contains brain MRI information on 216 marmosets aged between 1 and 10 years. During its release date, it is the largest public dataset worldwide. Further, it comprises multi contrast MRI images. In addition, 91 of 216 animals have corresponding ex vivo high-resolution MRI datasets. Our MRI database, which is available at the Brain/MINDS Data portal might help understand the effects of different factors, such as age, sex, body size, and fixation, on the brain. Moreover, it can contribute to and accelerate brain science studies worldwide.

neuroscience↗

bioRxiv2017

The Brain/MINDS 3D digital marmoset brain atlas

We present a new 3D digital brain atlas of the non-human primate, common marmoset monkey (Callithrix jacchus), with MRI and coregistered Nissl histology data. To the best of our knowledge this is the first comprehensive digital 3D brain atlas of the common marmoset having normalized multi-modal data, cortical and sub-cortical segmentation, and in a common file format (NIfTI). The atlas can be registered to new data, is useful for connectomics, functional studies, simulation and as a reference.\n\nThe atlas was based on previously published work but we provide several critical improvements to make this release valuable for researchers. Nissl histology images were processed to remove illumination and shape artifacts and then normalized to the MRI data. Brain region segmentation is provided for both hemispheres. The data is in the NIfTI format making it easy to integrate into neuroscience pipelines, whereas the previous atlas was in an inaccessible file format. We also provide cortical, mid-cortical and white matter boundary segmentations useful for visualization and analysis.

neuroscience↗