• Corpus ID: 234777844

Essential Metadata for 3D BRAIN Microscopy

  title={Essential Metadata for 3D BRAIN Microscopy},
  author={Alexander J. Ropelewski and Megan A. Rizzo and Jason R. Swedlow and Jan Huisken and Pavel Osten and Neda Khanjani and Kurt R Weiss and Vesselina D. Bakalov and Michelle L Engle and Lauren N Gridley and Michelle C Krzyzanowski and Tom Madden and Deborah R. Maiese and Justin Waterfield and David Williams and Carol Hamilton and Wayne Huggins},
Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining provide unprecedented opportunities to investigate brain structure and function. These experiments’ images make it possible to catalog brain cell types and define their location, morphology, and connectivity in a native context, leading to a better understanding of normal development and disease etiology. Consistent annotation of metadata is needed to provide the context necessary to understand… 
3 Citations

Tables from this paper

Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain
This review provides practical details for choosing methods including cell type specific labeling, sample preparation, microscopy modalities, image processing, and data analysis while developing and implementing high-resolution mapping methods.
Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data
An extension to BIDS for microscopy imaging data is presented, which includes comprehensible metadata definitions for hardware, image acquisition, and sample properties, to facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI.
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies
This work proposes that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging and can deliver truly findable, accessible, interoperable and reusable bioim imaging data.


Minimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data
The 4DN Imaging Standards Working Group has put forth a tiered system of microscopy calibration and metadata standards for images obtained through fluorescence microscopy, an extension of the OME data model and aims at increasing data fidelity, ease future analysis, and facilitate objective comparison of different datasets, experimental setups, and essays.
Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain
This new technique allows optical sectioning of fixed mouse brains with cellular resolution and can be used to detect single GFP-labeled neurons in excised mouse hippocampi and is ideally suited for high-throughput phenotype screening of transgenic mice and thus will benefit the investigation of disease models.
The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments
The Brain Imaging Data Structure (BIDS) is developed, a standard for organizing and describing MRI datasets that uses file formats compatible with existing software, unifies the majority of practices already common in the field, and captures the metadata necessary for most common data processing operations.
A global view of standards for open image data formats and repositories.
A shared, global view of criteria for these common, globally applicable guidelines and provisional proposals for open tools and resources that are available now and can provide a foundation for future development are presented.
Whole-animal functional and developmental imaging with isotropic spatial resolution
IsoView microscopy effectively doubles the penetration depth and provides subsecond temporal resolution for specimens 400-fold larger than could previously be imaged, and improves spatial resolution at least sevenfold and decreases resolution anisotropy at least threefold.
QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
The principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
Whole-brain functional imaging at cellular resolution using light-sheet microscopy
Light-sheet microscopy is used to record activity from the entire volume of the brain of the larval zebrafish in vivo at 0.8 Hz, capturing more than 80% of all neurons at single-cell resolution, demonstrating how this technique can be used to reveal functionally defined circuits across the brain.
Sharing brain mapping statistical results with the neuroimaging data model
This work introduces NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment, and provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices.
The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging
The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.