Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping: A pipeline for whole-brain structural and activity analyses.
Ontology highlight
ABSTRACT:
SUBMITTER: Jin DS
PROVIDER: S-EPMC10641303 | biostudies-literature | 2023 Oct
REPOSITORIES: biostudies-literature
Publications
Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping: A pipeline for whole-brain structural and activity analyses.
Jin David S DS Neelakantan Uma U Lacadie Cheryl M CM Chen Tianying T Rooney Brendan B Liu Yunqing Y Wu Weimiao W Wang Zuoheng Z Papademetris Xenophon X Hoffman Ellen J EJ
STAR protocols 20231026 4
Here, we present Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping, a user-friendly pipeline for the registration and analysis of whole-brain images in larval zebrafish. We describe steps for pre-processing, registration, quantification, and visualization of whole-brain phenotypes in zebrafish mutants of genes associated with neurodevelopmental and neuropsychiatric disorders. By utilizing BioImage Suite Web, an open-source software package originally developed for processing human ...[more]
Similar Datasets
Project description:In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open-source atlas containing molecular labels and definitions of anatomical regions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated extracellular signal–regulated kinase (ERK) as a readout of neural activity, we have developed a system to create and contextualize whole-brain maps of stimulus- and behavior-dependent neural activity. This mitogen-activated protein kinase (MAP)-mapping assay is technically simple, and data analysis is completely automated. Because MAP-mapping is performed on freely swimming fish, it is applicable to studies of nearly any stimulus or behavior. Here we demonstrate our high-throughput approach using pharmacological, visual and noxious stimuli, as well as hunting and feeding. The resultant maps outline hundreds of areas associated with behaviors.
| S-EPMC4710481 | biostudies-literature
Project description:Understanding the large-scale structural network formed by neurons is a major challenge in system neuroscience. A detailed connectivity map covering the entire brain would therefore be of great value. Based on diffusion MRI, we propose an efficient methodology to generate large, comprehensive and individual white matter connectional datasets of the living or dead, human or animal brain. This non-invasive tool enables us to study the basic and potentially complex network properties of the entire brain. For two human subjects we find that their individual brain networks have an exponential node degree distribution and that their global organization is in the form of a small world.
| S-EPMC1895920 | biostudies-literature
Project description:The zebrafish was used to assess the impact of social isolation on behaviour and brain function. As in humans and other social species, early social deprivation reduced social preference in juvenile zebrafish. Whole-brain functional maps of anti-social isolated (lonely) fish were distinct from anti-social (loner) fish found in the normal population. These isolation-induced activity changes revealed profound disruption of neural activity in brain areas linked to social behaviour, social cue processing, and anxiety/stress. Several of the affected regions are modulated by serotonin, and we found that social preference in isolated fish could be rescued by acutely reducing serotonin levels.
| S-EPMC7282805 | biostudies-literature
Project description:Studies of bipolar disorder (BD) suggest a genetic basis of the illness that alters brain function and morphology. In recent years, a number of genetic variants associated with BD have been identified. However, little is known about the associated genes, or brain circuits that rely upon their function. Using an anatomically comprehensive survey of the human transcriptome (The Allen Brain Atlas), we mapped the expression of 58 genes with suspected involvement in BD based upon their relationship to SNPs identified in genome wide association studies (GWAS). We then conducted a meta-analysis of structural MRI studies to identify brain regions that are abnormal in BD. Of 58 BD associated genes, 22 had anatomically distinct expression patterns that could be categorized into one of three clusters (C1-C3). Brain regions with the highest and lowest expression of these genes did not overlap strongly with anatomical sites identified as abnormal by structural MRI except in the parahippocampal gyrus, the inferior/superior temporal gyrus and the cerebellar vermis, regions where overlap was significant. Using the 22 genes in C1-C3 as reference points, additional genes with correlated expression patterns were identified and organized into sets based on similarity. Further analysis revealed that five of these gene sets were significantly associated with BD, suggesting that anatomical expression profile is correlated with genetic susceptibility to BD, particularly for genes in C2. Our data suggest that expression profiles of BD-associated genes do not explain the majority of structural abnormalities observed in BD, but may be useful in identifying new candidate genes. Our results highlight the complex neuroanatomical basis of BD, and reinforce illness models that emphasize impaired brain connectivity.
| S-EPMC4062532 | biostudies-literature
Project description:Identifying general principles of brain function requires the study of structure-function relationships in a variety of species. Zebrafish have recently gained prominence as a model organism in neuroscience, yielding important insights into vertebrate brain function. Although methods have been developed for mapping neural activity in larval animals, we lack similar techniques for adult zebrafish that have the advantage of a fully developed neuroanatomy and larger behavioral repertoire. Here, we describe a pipeline built around open-source tools for whole-brain activity mapping in freely swimming adult zebrafish. Our pipeline combines recent advances in histology, microscopy, and machine learning to capture cfos activity across the entirety of the adult brain. Images captured using light-sheet microscopy are registered to the recently created adult zebrafish brain atlas (AZBA) for automated segmentation using advanced normalization tools (ANTs). We used our pipeline to measure brain activity after zebrafish were subject to the novel tank test. We found that cfos levels peaked 15 minutes following behavior and that several regions containing serotoninergic, dopaminergic, noradrenergic, and cholinergic neurons were active during exploration. Finally, we generated a novel tank test functional connectome. Functional network analysis revealed that several regions of the medial ventral telencephalon form a cohesive sub-network during exploration. We also found that the anterior portion of the parvocellular preoptic nucleus (PPa) serves as a key connection between the ventral telencephalon and many other parts of the brain. Taken together, our work enables whole-brain activity mapping in adult zebrafish for the first time while providing insight into neural basis for the novel tank test.
| S-EPMC11370427 | biostudies-literature
Project description:AimsIn brain research, the histopathological examination of coronar whole-brain slides provides important insights into spatial disease characteristics. Regarding brain tumor research, this enables visualization of tumor heterogeneity, infiltration patterns and the relationship with the surrounding brain parenchyma. The precise correlation between radiological imaging and post-mortem brains is of special interest.New methodWe developed a wide-field slide scanner, comprising a microscope, a high-precision remotely controllable x-y-stage, a camera and a computer workstation, for automatically scanning uncommonly large formats. We analyzed whole brain slides of three patients and constructed cellularity heatmaps and fiber tract maps using a custom-made image processing pipeline.ResultsThe obtained cellularity heatmaps allow for distinguishing compact tumor (5714 ± 1786 cells/mm², mean ± standard deviation) from white matter (3581 ± 828 cells/mm²) and grey matter (2473 ± 716 cells/mm²). Compared to magnetic resonance imaging, the proposed histopathological work-up (i) reveals a larger zone of tumor infiltration around the compact tumor areas and (ii) shows how pre-existing tracts are displaced by the tumor bulk. Moreover, we highlight differences in the histological tumor growth pattern of two different radiological progression subtypes.Comparison with existing method(s)Compared to existing (commercial) solutions, our slide scanning solution is adaptable and cost-efficient. Moreover, we showcase potential clinical applications by mapping whole brain histology to magnetic resonance imaging.ConclusionsWe herein provide instructions on how to (i) construct a custom-built slide scanner capable of scanning arbitrary slide formats, (ii) automatically evaluate the cell density and (iii) perform fiber tracking on whole brain slides.
| S-EPMC6269083 | biostudies-literature
Project description:Atlases provide a framework for spatially mapping information from diverse sources into a common reference space. Specifically, brain atlases allow annotation of gene expression, cell morphology, connectivity, and activity. In larval zebrafish, advances in genetics, imaging, and computational methods now allow the collection of such information brain-wide. However, due to technical considerations, disparate datasets may use different references and may not be aligned to the same coordinate space. Two recent larval zebrafish atlases exemplify this problem: Z-Brain, containing gene expression, neural activity, and neuroanatomical segmentations, was acquired using immunohistochemical stains, while the Zebrafish Brain Browser (ZBB) was constructed from live scans of fluorescent reporters in transgenic larvae. Although different references were used, the atlases included several common transgenic patterns that provide potential "bridges" for transforming each into the other's coordinate space. We tested multiple bridging channels and registration algorithms and found that the symmetric diffeomorphic normalization algorithm improved live brain registration precision while better preserving cell morphology than B-spline-based registrations. Symmetric diffeomorphic normalization also corrected for tissue distortion introduced during fixation. Multi-reference channel optimization provided a transformation that enabled Z-Brain and ZBB to be co-aligned with precision of approximately a single cell diameter and minimal perturbation of cell and tissue morphology. Finally, we developed software to visualize brain regions in 3 dimensions, including a virtual reality neuroanatomy explorer. This study demonstrates the feasibility of integrating whole brain datasets, despite disparate reference templates and acquisition protocols, when sufficient information is present for bridging. Increased accuracy and interoperability of zebrafish digital brain atlases will facilitate neurobiological studies.
| S-EPMC5597853 | biostudies-literature
Project description:MotivationRecent brain mapping efforts are producing large-scale whole-brain images using different imaging modalities. Accurate alignment and delineation of anatomical structures in these images are essential for numerous studies. These requirements are typically modeled as two distinct tasks: registration and segmentation. However, prevailing methods, fail to fully explore and utilize the inherent correlation and complementarity between the two tasks. Furthermore, variations in brain anatomy, brightness, and texture pose another formidable challenge in designing multi-modal similarity metrics. A high-throughput approach capable of overcoming the bottleneck of multi-modal similarity metric design, while effective leveraging the highly correlated and complementary nature of two tasks is highly desirable.ResultsWe introduce a deep learning framework for joint registration and segmentation of multi-modal brain images. Under this framework, registration and segmentation tasks are deeply coupled and collaborated at two hierarchical layers. In the inner layer, we establish a strong feature-level coupling between the two tasks by learning a unified common latent feature representation. In the outer layer, we introduce a mutually supervised dual-branch network to decouple latent features and facilitate task-level collaboration between registration and segmentation. Since the latent features we designed are also modality-independent, the bottleneck of designing multi-modal similarity metric is essentially addressed. Another merit offered by this framework is the interpretability of latent features, which allows intuitive manipulation of feature learning, thereby further enhancing network training efficiency and the performance of both tasks. Extensive experiments conducted on both multi-modal and mono-modal datasets of mouse and human brains demonstrate the superiority of our method.Availability and implementationThe code is available at https://github.com/tingtingup/DCRS.
| S-EPMC11543610 | biostudies-literature
Project description:BackgroundIntegration of medicinal chemistry data from numerous public resources is an increasingly important part of academic drug discovery and translational research because it can bring a wealth of important knowledge related to compounds in one place. However, different data sources can report the same or related compounds in various forms (e.g., tautomers, racemates, etc.), thus highlighting the need of organising related compounds in hierarchies that alert the user on important bioactivity data that may be relevant. To generate these compound hierarchies, we have developed and implemented canSARchem, a new compound registration and standardization pipeline as part of the canSAR public knowledgebase. canSARchem builds on previously developed ChEMBL and PubChem pipelines and is developed using KNIME. We describe the pipeline which we make publicly available, and we provide examples on the strengths and limitations of the use of hierarchies for bioactivity data exploration. Finally, we identify canonicalization enrichment in FDA-approved drugs, illustrating the benefits of our approach.ResultsWe created a chemical registration and standardization pipeline in KNIME and made it freely available to the research community. The pipeline consists of five steps to register the compounds and create the compounds' hierarchy: 1. Structure checker, 2. Standardization, 3. Generation of canonical tautomers and representative structures, 4. Salt strip, and 5. Generation of abstract structure to generate the compound hierarchy. Unlike ChEMBL's RDKit pipeline, we carry out compound canonicalization ahead of getting the parent structure, similar to PubChem's OpenEye pipeline. canSARchem has a lower rejection rate compared to both PubChem and ChEMBL. We use our pipeline to assess the impact of grouping the compounds in hierarchies for bioactivity data exploration. We find that FDA-approved drugs show statistically significant sensitivity to canonicalization compared to the majority of bioactive compounds which demonstrates the importance of this step.ConclusionsWe use canSARchem to standardize all the compounds uploaded in canSAR (> 3 million) enabling efficient data integration and the rapid identification of alternative compound forms with useful bioactivity data. Comparison with PubChem and ChEMBL pipelines evidenced comparable performances in compound standardization, but only PubChem and canSAR canonicalize tautomers and canSAR has a slightly lower rejection rate. Our results highlight the importance of compound hierarchies for bioactivity data exploration. We make canSARchem available under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0) at https://gitlab.icr.ac.uk/cansar-public/compound-registration-pipeline .
| S-EPMC9148294 | biostudies-literature
Project description:The field of macro-imaging has grown considerably with the appearance of innovative clearing methods and confocal microscopes with lasers capable of penetrating increasing tissue depths. The ability to visualize and model the growth of whole organs as they develop from birth, or with manipulation, disease or injury, provides new ways of thinking about development, tissue-wide signaling, and cell-to-cell interactions. The zebrafish (Danio rerio) has ascended from a predominantly developmental model to a leading adult model of tissue regeneration. The unmatched neurogenic and regenerative capacity of the mature central nervous system, in particular, has received much attention, however tools to interrogate the adult brain are sparse. At present there exists no straightforward methods of visualizing changes in the whole adult brain in 3-dimensions (3-D) to examine systemic patterns of cell proliferation or cell populations of interest under physiological, injury, or diseased conditions. The method presented here is the first of its kind to offer an efficient step-by-step pipeline from intraperitoneal injections of the proliferative marker, 5-ethynyl-2'-deoxyuridine (EdU), to whole brain labeling, to a final embedded and cleared brain sample suitable for 3-D imaging using optical projection tomography (OPT). Moreover, this method allows potential for imaging GFP-reporter lines and cell-specific antibodies in the presence or absence of EdU. The small size of the adult zebrafish brain, the highly consistent degree of EdU labeling, and the use of basic clearing agents, benzyl benzoate, and benzyl alcohol, makes this method highly tractable for most laboratories interested in understanding the vertebrate central nervous system in health and disease. Post-processing of OPT-imaged adult zebrafish brains injected with EdU illustrate that proliferative patterns in EdU can readily be observed and analyzed using IMARIS and/or FIJI/IMAGEJ software. This protocol will be a valuable tool to unlock new ways of understanding systemic patterns in cell proliferation in the healthy and injured brain, brain-wide cellular interactions, stem cell niche development, and changes in brain morphology.
| S-EPMC5776138 | biostudies-literature