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

Abstract

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.

MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy

“…We designed MorphoFeatures to enable unbiased exploration of morphological variability in the animal on both cellular and tissue level; and indeed our training procedure yields 480 features that extensively describe each cell in terms of its cytoplasm and nucleus shape, coarse texture, and fine texture (80 features for each category). The features can be found at https://github.com/kreshuklab/MorphoFeatures.git ; the feature table can be directly integrated with the Platynereis atlas of Vergara et al, 2021 through the MoBIE plugin ( Pape et al, 2022 ) in Fiji ( Schindelin et al, 2012 ).…”

“…In the first clustering round, we split cells into 15 broad morphological groups ( Figure 3B ). Cluster content could be revealed through available annotations and visualisation with the PlatyBrowser ( Pape et al, 2022 ; Figure 3B ): Clusters 1–8 represent different groups of neurons; 9–11 epithelial cells; 12 and 13 are muscles; 14 midgut cells; while cluster 15 was further subclustered into secretory cells (subcluster 1) and ciliary band cells (subcluster 2). MorphoFeatures can thus guide the morphological exploration of a whole-animal volume, facilitating the discovery and annotation of morphologically coherent groups of cells ( Figure 3B ).…”

“…We used matplotlib ( Hunter, 2007 ) and seaborn ( Waskom, 2021 ) for plotting the data, MoBIE ( Pape et al, 2022 ) for visualising cells in the EM volume, and vedo ( Musy et al, 2022 ) for visualising meshed cells and tissues.…”

Targeted volume Correlative Light and Electron Microscopy of an environmental marine microorganism

“…As datasets of this sort are rare and precious for the community, we believe it is important to make them available. Thus, the raw dataset as well as the segmentations described in this study are accessible in an easily browsable format using Fiji through the Mobie plugin (Pape et al, 2022).…”

“…The Fiji plugin MoBIE (Pape et al, 2022) can be used to explore the different datasets. Instructions for plugin download and installation can be found using the following link: https://github.com/mobie/mobie-viewer-fiji.…”