The BioImage Archive - building a home for life-sciences microscopy data

Hartley, Matthew; Kleywegt, Gerard J.; Patwardhan, Ardan; Sarkans, Ugis; Swedlow, Jason R.; Brāzma, Alvis

doi:10.1101/2021.12.17.473169

Cited by 11 publications

(11 citation statements)

References 34 publications

(26 reference statements)

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“…AF2 models and associated statistics will be deposited in the University of Cambridge Data Repository (TBA). Raw electron microscopy images, processed data and final models will be deposited in the University of Cambridge Data Repository (TBA) and the Electron Microscopy Public Image Archive EMPIAR (79).…”

Section: Data Availabilitymentioning

confidence: 99%

Altered plasma membrane abundance of the sulfatide-binding protein NF155 links glycosphingolipid imbalances to demyelination

McKie

Nicholson

Smith

et al. 2022

Preprint

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Myelin is a multi-layered membrane that tightly wraps neuronal axons enabling efficient, high-speed signal propagation. The axon and myelin sheath form tight contacts, mediated by specific plasma membrane proteins and lipids, and disruption of these contacts causes devastating demyelinating diseases. Using two cell-based models of demyelinating sphingolipidoses, we demonstrate that altered lipid metabolism changes the abundance of specific plasma membrane proteins. These altered membrane proteins have known roles in cell adhesion and signalling, with several implicated in neurological diseases. The cell surface abundance of the adhesion molecule Neurofascin, a protein critical for the maintenance of myelin-axon contacts, changes following disruption to sphingolipid metabolism. This provides a direct molecular link between altered lipid abundance and myelin stability. We show that the Neurofascin isoform NF155, but not NF186, interacts directly and specifically with the sphingolipid sulfatide via multiple binding sites and that this interaction requires the full-length extracellular domain of NF155. We demonstrate that NF155 adopts an S-shaped conformation and preferrentially binds sulfatide-containing membranes in cis, with important implications for protein arrangement in the tight axon-myelin space. Our work links glycosphingolipid imbalances to disturbance of membrane protein abundance and demonstrates how this may be driven by direct protein-lipid interactions, providing a mechanistic framework to understand the pathogenesis of galactosphingolipidoses.

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Section: Data Availabilitymentioning

confidence: 99%

Altered plasma membrane abundance of the sulfatide-binding protein NF155 links glycosphingolipid imbalances to demyelination

McKie

Nicholson

Smith

et al. 2022

Preprint

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“…Sharing of 3D imaging data to a similar extend as currently achieved for sequencing data will be important. The BioImage Archive, a central archival system at EMBL‐EBI (Hartley et al , 2022), now provides infrastructure for archiving and accessing existing imaging data. Although already a highly commendable resource, supporting patient‐identifiable data in the future could further advance its application in cancer research.…”

Section: Introductionmentioning

confidence: 99%

3D imaging for driving cancer discovery

et al. 2022

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Our understanding of the cellular composition and architecture of cancer has primarily advanced using 2D models and thin slice samples. This has granted spatial information on fundamental cancer biology and treatment response. However, tissues contain a variety of interconnected cells with different functional states and shapes, and this complex organization is impossible to capture in a single plane. Furthermore, tumours have been shown to be highly heterogenous, requiring large-scale spatial analysis to reliably profile their cellular and structural composition. Volumetric imaging permits the visualization of intact biological samples, thereby revealing the spatio-phenotypic and dynamic traits of cancer. This review focuses on new insights into cancer biology uniquely brought to light by 3D imaging and concomitant progress in cancer modelling and quantitative analysis. 3D imaging has the potential to generate broad knowledge advance from major mechanisms of tumour progression to new strategies for cancer treatment and patient diagnosis. We discuss the expected future contributions of the newest imaging trends towards these goals and the challenges faced for reaching their full application in cancer research.

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“…Overall, MoBIE enables life scientists to seamlessly access, explore and share their often massive microscopy data through all stages of the lifetime of a project in a convenient Fiji plugin. We are working with online archives to deploy MoBIE to support on-demand access to existing scientific image data and have already implemented two prototypes for this kind of access, with the BioImage Archive 24 and with Open Organelle 25 . See Methods for details.…”

mentioning

confidence: 99%

“…The second is the BioImage Archive 24 , an image data repository hosted by the European Bioinformatics Institute. It accepts image data submissions associated with publications in the life-sciences.…”

mentioning

confidence: 99%

MoBIE: A Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data

Pape

Meechan

Moreva

et al. 2022

Preprint

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Facing the challenge of exploring and sharing multi-terabyte, multi-modal and multi-scale image data of heterogeneous dimensionality, we developed MoBIE, a Fiji plugin that provides rich visualization features to enable browsing data from numerous biomedical applications on a standard laptop computer. MoBIE also supports segmentations, associated measurements and annotations. Users can configure complex views of datasets, share them with collaborators, and use them for interactive figure panels. The MoBIE plugin also offers a convenient interface for converting data into compatible data formats; an additional Python library facilitates managing diverse MoBIE projects.

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The BioImage Archive - building a home for life-sciences microscopy data

Cited by 11 publications

References 34 publications

Altered plasma membrane abundance of the sulfatide-binding protein NF155 links glycosphingolipid imbalances to demyelination

Altered plasma membrane abundance of the sulfatide-binding protein NF155 links glycosphingolipid imbalances to demyelination

3D imaging for driving cancer discovery

MoBIE: A Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data

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